the structure of the nuclear pore complex
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BI80CH26-Hoelz ARI 16 May 2011 12:36
The Structure of the NuclearPore ComplexAndre Hoelz,1 Erik W. Debler,2
and Gunter Blobel2,3
1Division of Chemistry and Chemical Engineering, California Institute of Technology,Pasadena, California 91125; email: hoelz@caltech.edu2Laboratory of Cell Biology and 3Howard Hughes Medical Institute, The RockefellerUniversity, New York, NY 10065
Annu. Rev. Biochem. 2011. 80:613–43
First published online as a Review in Advance onApril 12, 2011
The Annual Review of Biochemistry is online atbiochem.annualreviews.org
This article’s doi:10.1146/annurev-biochem-060109-151030
Copyright c© 2011 by Annual Reviews.All rights reserved
0066-4154/11/0707-0613$20.00
Keywords
α-helical solenoid, binding promiscuity, β-propeller,nucleocytoplasmic transport, nucleoporin, membrane coats
Abstract
In eukaryotic cells, the spatial segregation of replication and transcrip-tion in the nucleus and translation in the cytoplasm imposes the require-ment of transporting thousands of macromolecules between these twocompartments. Nuclear pore complexes (NPCs) are the sole gatewaysthat facilitate this macromolecular exchange across the nuclear enve-lope with the help of soluble transport receptors. Whereas the mobiletransport machinery is reasonably well understood at the atomic level,a commensurate structural characterization of the NPC has only be-gun in the past few years. Here, we describe the recent progress towardthe elucidation of the atomic structure of the NPC, highlight emerg-ing concepts of its underlying architecture, and discuss key outstandingquestions and challenges. The applied structure determination as wellas the described design principles of the NPC may serve as paradigmsfor other macromolecular assemblies.
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NPC: nuclear porecomplex
EM: electronmicroscopy
Contents
INTRODUCTION . . . . . . . . . . . . . . . . . . 614Nucleoporin Family. . . . . . . . . . . . . . . . 614Functions of the Nuclear Pore
Complex . . . . . . . . . . . . . . . . . . . . . . . 615NUCLEAR PORE COMPLEX
ARCHITECTURE BYELECTRON MICROSCOPY . . . . . 617
NUCLEOPORIN STRUCTURESOF THE SYMMETRIC CORE . . . 619Coat Nucleoporins: Members of the
Heptameric Nup84 Complex . . . . 620Common Evolutionary Origin of the
Nuclear Pore Complex andOther Membrane Coats . . . . . . . . . 624
Adaptor Nucleoporins: Membersof the Heteromeric Nic96Complex . . . . . . . . . . . . . . . . . . . . . . . 625
Channel Nucleoporins: Members ofthe Heterotrimeric Nsp1Complex . . . . . . . . . . . . . . . . . . . . . . . 626
TRANSPORT FACTORFG-REPEATINTERACTIONS . . . . . . . . . . . . . . . . 626β-Karyopherin FG-Repeat
Interactions. . . . . . . . . . . . . . . . . . . . . 626RanGDP Import Factor
NTF2-FG-RepeatInteractions. . . . . . . . . . . . . . . . . . . . . 628
mRNA Export FactorTAP-p15-FG-RepeatInteractions. . . . . . . . . . . . . . . . . . . . . 628
STRUCTURES OF ASYMMETRICNUCLEOPORINS . . . . . . . . . . . . . . . 629Cytoplasmic Filament Nucleoporins
and Associated mRNA ExportFactors . . . . . . . . . . . . . . . . . . . . . . . . . 629
Nuclear Basket Nucleoporins . . . . . . . 631MODELS OF THE SYMMETRIC
NUCLEAR PORE COMPLEXCORE . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631
INTRODUCTION
A eukaryotic cell is subdivided into spatiallyand functionally distinct, membrane-enclosed
compartments that enable it to concomitantlyperform numerous cellular tasks in specializedmicroenvironments. This subcellular divisionis achieved by intricate intracellular membranesystems. The double membrane of the nuclearenvelope segregates the nucleoplasm contain-ing the genetic material from the cytoplasm.Whereas the nucleus is the site of transcription,the synthesized RNA molecules have to leavethe nucleus to be translated into proteins byribosomes in the cytoplasm. In addition toprotecting the DNA from harmful effectsin the cytoplasm, the spatial separation oftranscription and translation imposes anotherlevel of regulation in the flow of informationfrom DNA to protein.
Nuclear pore complexes (NPCs) are em-bedded in pores of the nuclear envelope andconstitute large aqueous transport channelsthat mediate and regulate the bidirectionalexchange of macromolecules between the nu-cleus and cytoplasm. The NPC represents oneof the largest and most complex proteinaceousassemblies in the eukaryotic cell. Since itsdiscovery more than half a century ago, thestructure of the NPC has been extensivelyinvestigated by electron microscopy (EM).Atomic-resolution analysis of the entire NPCby X-ray crystallography has been hindered byits sheer size, dynamic and flexible nature, andthe difficulties in purifying sufficient amountsof homogeneous material. More recently, thecharacterization of the molecular compositionof the NPC and the establishment of its mod-ular architecture have enabled the structuredetermination of individual domains, proteins,and their subcomplexes at atomic resolutionby X-ray crystallography, which delineates a“divide-and-conquer” approach toward thecomplete atomic structure of the NPC.
Nucleoporin Family
The NPC is composed of a set of approx-imately 30 different proteins, collectivelytermed nucleoporins, that are conserved inevolutionarily distant eukaryotes ranging fromyeast to human (1–4). Reflecting a high degree
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Nucleoporins:a family of ∼30evolutionarilyconserved proteinsthat construct theNPC. Most of themare termed Nupfollowed by theirmolecular mass
POM: an integralmembrane protein ofthe pore membranedomain of the nuclearenvelope
Nuclear basket:filaments that areattached to the nuclearface of the symmetricNPC core and that arebundled by a distalring
Cytoplasmicfilaments: filamentsattached to thecytoplasmic face of thesymmetric NPC corethat serve as dockingsites for transportfactors
Phenylalanine-glycine (FG) repeats:repeats in unstructurednucleoporin regionsthat form thepermeability barrierand serve as dockingsites for karyopherins
β-propeller domain:a protein fold that iscomposed of 4–8circularly arrangedstructural units calledblades that arecomposed of 4antiparallel β-strands
Karyopherins (Kaps):transport factors thatrecognize nuclearimport and exportsignal sequences incargo and facilitatetransport through theNPC
of internal symmetry, each nucleoporin occursin multiple copies, resulting in ∼500–1,000protein molecules in the fully assembledNPC. Using analytical ultracentrifugation, amolecular mass of ∼66 MDa was determinedfor isolated intact NPCs of the invertebrateSaccharomyces cerevisiae (5), whereas a molecularmass of ∼112 MDa was deduced for the NPCof the vertebrate Xenopus laevis from scanningtransmission EM (6). The ratio of the differentnucleoporins within a single NPC has been es-timated by semiquantitative methods. Becausethe results have been largely inconsistent,most likely owing to technical limitations,the absolute stoichiometry of all nucleoporinsremains unknown (2, 3, 7). Most nucleoporinsare denoted “Nup” followed by a number thatin most cases refers to their molecular mass.Because of the molecular mass differencesin various species, a uniform nomenclaturefor nucleoporins does not exist. However,based on their approximate localization withinthe NPC, the nucleoporins can be classifiedinto six categories: (a) integral membraneproteins of the pore membrane domain ofthe nuclear envelope (POMs), (b) membrane-apposed coat nucleoporins, (c) adaptornucleoporins, (d ) channel nucleoporins,(e) nuclear basket nucleoporins, and ( f ) cyto-plasmic filament nucleoporins (Figures 1 and2) (8).
Homology modeling suggests that nucle-oporins are primarily constructed from oneor more of the following structural units: α-helical regions, β-propellers, and unstructuredphenylalanine-glycine (FG) repeats (Figure 3)(9). β-propellers are ubiquitous disk-shapeddomains with an overall diameter of ∼70 Aand a thickness of ∼40 A (10). The canonicalβ-propeller core is generated by four to eightblades that are circularly arranged. Each bladeconsists of four antiparallel β-strands, whichby convention are termed A to D from theinside to the outside of the β-propeller. Sofar, atomic models for six of the nine predictedβ-propellers in yeast nucleoporins have beenexperimentally determined (Figure 3) (8,11–20). Whereas the β-propeller core provides
a sturdy structural scaffold, the structuresuncovered numerous unexpected decorativefeatures that play a central role in protein-protein interactions within the NPC. Thestructural characterization of 8 of the 25 pre-dicted α-helical regions of yeast nucleoporinsrevealed a set of diverse and novel folds withsurprising properties that could not have beenanticipated by homology modeling (Figure 3)(8, 14–19, 21–25). These domains are almostexclusively composed of α-helices arranged ina zigzag fashion and feature diverse topologies,which strikingly differ from the canonicalsuperhelical solenoids typically observed intransport receptors (26, 27).
Functions of the NuclearPore Complex
The principle function of the NPC is thefacilitation of nucleocytoplasmic traffic, whileat the same time generating a diffusion barrierto separate the cytoplasm from the nuclearcompartment. Diffusion channels with a cal-culated diameter of ∼90–100 A allow the freepassage of macromolecules of up to ∼40 kDa,whereas larger cargoes with a diameter ofup to ∼390 A require active translocation bytransport receptors (Supplemental Movies 1and 2) (28–30). (Follow the SupplementalMaterial link from the Annual Reviews homepage at http://www.annualreviews.org.) Thediffusion barrier is formed by extended nativelyunfolded nucleoporin segments that containnumerous FG repeats. The exact nature ofthe permeability barrier remains a heavily de-bated topic (31–39). Because of the intrinsiclyunstructured nature of the FG repeats, X-raycrystallography can only contribute to a minorextent to resolve this issue.
FG repeats also serve as docking sitesfor transport receptors, collectively termedkaryopherins (kaps) (also known as importinsand exportins), that “ferry” the cargo throughthe permeability barrier (26, 27, 40–47). Nu-cleocytoplasmic transport is dictated by shortsequence elements in cargo molecules, whichare recognized by karyopherins. A nuclear
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a
65°
FG repeats
POMs
Coat nucleoporins
Adaptor nucleoporins
Channel nucleoporins
Cytoplasmicfilaments
Nuclear basket
Nuclearenvelope
b
Cytoplasmic view
25°
Side view
Cargo intransit
Figure 1Overall structure of the nuclear pore complex (NPC). (a) Cryo-electron tomographic reconstruction of theDictyostelium discoideum NPC [Electron Microscopy Data Bank (EMDB) code 1097, Reference 81]. Thecytoplasmic filaments, the symmetric core, and the nuclear basket are colored in cyan, orange, and purple,respectively. (b) A schematic model of the NPC. The four concentric cylinders are composed of integral poremembrane proteins (POMs), coat nucleoporins, adaptor nucleoporins, and channel nucleoporins. Nativelyunfolded phenylalanine-glycine (FG) repeats of a number of nucleoporins make up the transport barrier inthe central channel and are indicated by a transparent plug.
Ran: a small GTPasethat is a keycomponent for thegeneration of thedirectionality ofnucleocytoplasmictransport
localization sequence is responsible for import,whereas a nuclear export sequence is used forexport. β-karyopherins (β-kaps) interact withcargo molecules either directly or indirectlyvia an adaptor karyopherin termed α-kap. Thedirectionality of transport is governed by aconcentration gradient of RanGTP, which ismaintained at a high level inside the nucleus
but at a low level in the cytoplasm (26, 45,47). Ran can adopt two distinct conformationsthat depend on the bound nucleotide (GTP orGDP). RanGTP not only disassembles importcomplexes upon entrance into the nucleus,but also promotes the assembly of exportcomplexes inside the nucleus. Upon arrival atthe cytoplasmic side of the NPC, these export
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complexes are disassembled by removal ofRanGTP with the help of proteins thatare tethered to the cytoplasmic filaments(Supplemental Movie 2).
The mobile transport machinery, the assem-bly and disassembly of transport complexes, aswell as cargo recognition have been extensivelystudied (26, 27, 40, 45–47). By contrast, thepassage of large cargo, such as preribosomalparticles, or the import of integral membraneproteins that are destined for the inner nu-clear membrane, are less well understood(Supplemental Movies 3 and 4). (Followthe Supplemental Material link from theAnnual Reviews home page at http://www.annualreviews.org.) Clearly, the NPC is notmerely a static conduit with a permeabilitybarrier but a dynamic transport organellethat must undergo substantial structural rear-rangements to permit these transport events(30, 48–51).
In addition to enabling nucleocytoplasmictransport, the NPC and its components areinvolved in numerous other cellular functions,such as chromatin organization, replication-coupled DNA repair, and regulation of gene ex-pression (52–61). In eukaryotes with open mito-sis, some nucleoporins have a well-documentedrole during cell division (62). Duringprometaphase, the NPC dismantles into dis-tinct subcomplexes from which it reassembles atthe completion of telophase (1, 63–65). Similarsubcomplexes can also be dissected biochem-ically from fully assembled interphase NPCsand from NPCs of eukaryotes with closed mi-tosis (66, 67). The best-characterized exampleof an NPC component with a cell cycle–specific function is the vertebrate Nup107–160complex that is targeted to kinetochores duringmitosis, where it functions in spindle assembly(63, 65, 68–70). On the basis of the central anddiverse roles of the NPC in cellular physiology,it is not surprising that defects in the NPC orits components are linked to a diverse set ofdiseases, including hematological neoplasms,heart arrhythmia, and primary biliary cirrhosis(71–73).
Symmetric nucleoporins Asymmetric nucleoporins
Yeast Human
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Gp210POM121
NDC1
Nup62
Nup58Nup45
Nup93Nup205Nup188
Nup107Nup133
Seh1Nup75Nup160Sec13Nup96
Nup37Nup43
Nup54
- - -- - -
Nup155
Nup35
POM152POM34NDC1
Nsp1Nup57
Nic96Nup192Nup188Nup157Nup170Nup53Nup59
Nup84Nup133
Seh1Nup85Nup120Sec13Nup145C
- - -- - -
- - -- - -
Nup49
POM
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Yeast Human
Gle1Dbp5
Nup2Nup1
Nup60
Nup82Nup159
Nup100Nup145N
Nup116
Nup42
Mlp1Mlp2
Gle2
- - -
- - -
}
Ddx19Gle1
Nup50Nup153
Nup88
CG1
Nup98
Nup358
ALADIN
Rae1
Nup214
- - -
TPR}Nuc
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Chan
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Figure 2Molecular composition of the yeast and human nuclear pore complexes(NPCs). Symmetric nucleoporins form the core region and are equallydistributed on the cytoplasmic and nucleoplasmic halves of the NPC.Asymmetric nucleoporins form the nuclear basket and the cytoplasmicfilaments that serve as docking sites for transport factors and include associatedmRNA export factors. The nucleoporin classification is as described inFigure 1b. POM, an integral membrane protein.
NUCLEAR PORE COMPLEXARCHITECTURE BY ELECTRONMICROSCOPY
Since the discovery of pores in the nuclearenvelope in 1950 (74) and of the embeddedNPCs thereafter (75), the overall architectureand characteristics of the NPC have been ex-tensively investigated by EM. Initially observedas cylindrical formations that penetrate thenuclear envelope with a diameter of ∼1,000 A(75), a more detailed study established an eight-fold rotational symmetry of NPCs along theirnucleocytoplasmic axes (76). Occasionally,
www.annualreviews.org • Nuclear Pore Complex Structure 617
Supplemental Material
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~760
974 1,012
α/β-region RRM
RanBD
Gle11 538
N C
B α/β-region
U1 726460
N CNup84 α-helical solenoid 507
Nup159
Nup192 N C1 1,683
α-helical
Nup1881 1,655
N Cα-helical
Nup821 713452490
N Cβ-propeller α-helicalU
FG repeats αN CNup421 380 430
1 570 814 959FG repeats U CTDN CNup100
1 605209 458Nup145N FG repeats APDUN C
1 686115 166 1,113967N CFG repeats UGNup116
Seh1 N C1 349
β-propeller
1 57044 101 744N CNup85 DIM α-helical solenoid α-helicalU
N Cβ-propeller Insert α-helical domain α-helicalUNup1201 729382 1,037487460
Sec13 N C1 297
β-propeller
1 555125 183 711N CDIMU α-helical solenoid α-helicalNup145C
1 1,15752056N Cβ-propeller α-helical domainUNup133
Nic96 N1 839190
Cα α-helical domain
1 1,391~680Nup157 N Cβ-propeller α-helical
1 1,502~650 979~180Nup170 N CU β-propeller α-helical domain
Nup53 N C1 475
Nup59 N C1 528
Nsp18235911 631
N CFG repeats α-helicalU
Nup49 N Cα-helicalFG repeats2381 472
2561 541Nup57 N Cα-helicalFG repeats
2491 655α-helicalNDC1 N C
2991 147POM34 N C
1,3371 208POM152 N Cβ-strand region
1 48271 296NDbp5 CNTE Domain 1 Domain 2
N1 1,4601,103 1,177876387
β-propeller α-helicalFG repeats U DID C
Nup11,0761 ~400
N Cα/β-region FG repeats
Nup2 FG repeatsN C7201 ~245 ~55051
Mlp1 N1,8751
C
Mlp21,6791
N C
Nup605391
N Cα/β-region
α-helical
α-helical
β-propellerN CGle21 365
Cyto
plas
mic
filam
ents
Nuc
lear
bas
ket
POM
sCh
anne
lnu
cleo
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nsA
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or n
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Coat
nuc
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α-helical
355251
B
CTD
U α-helical
U
α/β-region
RRM271 397
α-helical region
β-propeller/β-strand region
Unstructured (U)
FG repeat region
Transmembrane helices
Fragments whose crystal structuresare experimentally determined:
Yeast
α/β-region
α/β-region
MammalianYeast and mammalian
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Pore membranedomain: the sectionof the nuclear envelopewhere inner and outernuclear membranesare fused to form thenuclear pores
Symmetric NPCcore: the NPC corehas an eightfoldrotational symmetryalong thenucleocytoplasmic axisand twofold rotationalsymmetryperpendicular to it
NPCs with nine- and tenfold rotationalsymmetry have been observed, suggesting asomewhat flexible and modular assembly (77).Three-dimensional (3D) reconstructions to∼90 A, computed from Xenopus NPCs em-bedded in nuclear envelopes, identified severaldiscrete units within the NPC (78): two coaxialrings with one on the cytoplasmic peripheryand the other on the nuclear periphery; eightelongated structures termed spokes connectingthe two rings; and a spherical particle termedcentral plug in the transport channel, whichwas subsequently shown to represent cargo intransit (79–81). Apparent twofold axes perpen-dicular to the octad axis suggest a symmetriccore of the NPC that is constructed fromtwo equal but oppositely facing halves (78).Attached to the symmetric core are cytoplasmicfilaments and a basket-like structure on the nu-cleoplasmic face, both of which provide bindingsites for cargo (79, 82–85). In vertebrate NPCs,peripheral or lateral channels with an averagediameter of ∼100 A were described (86), butwere significantly less pronounced in a cryo-EM reconstruction of detergent-extracted andmembrane-associated NPCs (87). Moreover,the latter study identified a lumenal ring, whichwas proposed to be responsible for anchoringthe NPC within the nuclear envelope pore, anddescribed an intrinsic conformational flexibilityof the spokes (87). Structural plasticity andflexibility, which are thought to be criticalaspects of NPC function, were also uncoveredin another analysis of Xenopus NPCs (88).
The first NPC reconstruction determinedby cryo-electron tomography (cryo-ET) wasperformed on native NPCs from Xenopusand revealed the “spongy” symmetric coreframework (80). NPCs of intact nuclei from
Dictyostelium discoideum show structural rear-rangements of the NPC scaffold in responseto cargo translocation (Figure 1a) (81). A newcryo-ET image-processing strategy yielded thehighest resolution (58 A) of the NPC to date(51). Tomograms recorded in the presence ofgold-labeled cargo outlined the trajectory ofimport cargo (51). The latest cryo-ET on theXenopus NPC revealed a fused concentric ringarchitecture and provided refined overall NPCdimensions, i.e., ∼1,250 A for the diameter,∼950 A for the height, and ∼550 A for thediameter of the central channel (89).
In comparison to the vertebrate NPCs, theNPC of S. cerevisiae is considerably smaller,with a comparable outer diameter (∼960 A), butwith a height that is less than half of its verte-brate counterpart (∼350 A) (90). This discrep-ancy correlates with the determined thicknessof the yeast and vertebrate nuclear envelopes of∼300 A (90) and ∼600 A (87), respectively. No-tably, lateral channels have not been observedin the more compact architecture of the yeastNPC (90). Despite these differences, a compar-ison of NPC structures, as determined by EMacross vertebrates and invertebrates, suggeststhat the overall architecture is well conserved(48, 86, 90).
NUCLEOPORIN STRUCTURESOF THE SYMMETRIC CORE
The pore membrane domain of the nuclear en-velope harbors three POMs that anchor thesymmetric NPC core (Figure 1b). In additionto their transmembrane helices, they containlarge regions that extend toward the lumenaland pore sides of the membrane. In NDC1
←−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−Figure 3Domain architecture of yeast nucleoporins. Domain borders are indicated by residue numbers. NTE, N-terminal extension;U, unstructured; FG repeat, phenylalanine-glycine (FG) repeat; DID, dynein light-chain interacting domain; CTD, C-terminaldomain; G, Gle2-binding sequence (GLEBS); APD, autoproteolytic domain; DIM, domain invasion motif; RRM, RNA-recognitionmotif; B, karyopherin-binding domain; RanBD, Ran-binding domain; POM, an integral membrane protein. The bars above thedomain organizations mark fragments whose crystal structures are experimentally determined (black, yeast; red, mammalian; green, yeastand mammalian). Notably, the nucleoporins Nup1 and Nup2 do not follow the common nomenclature because the numbers 1 and 2 donot refer to their molecular weight.
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α-helical solenoid:a protein fold that iscomposed of α-helicesarranged in a zigzagfashion
and POM34, these regions are located primar-ily on the pore side, whereas the major partof POM152 reaches into the lumen of the nu-clear envelope. Most recently, a fourth trans-membrane nucleoporin termed POM33 wasdiscovered (91). The remainder of the sym-metric core is composed of seven coat nucle-oporins, seven adaptor nucleoporins, and threechannel nucleoporins (Figure 2). The coat andadaptor nucleoporins are mostly composed ofβ-propellers and α-helical domains, whereasthe channel nucleoporins contain extensive na-tively unfolded FG-repeat regions. Altogether,the symmetric NPC core comprises ∼20distinct proteins.
Coat Nucleoporins: Members of theHeptameric Nup84 Complex
In yeast, the seven coat nucleoporins assembleinto the well-defined Nup84 complex, termedafter one of its components. This subcom-plex consists of Nup84, Nup120, Nup85,Nup145C, Sec13, Seh1, and Nup133 (92–95).Negative-stain two-dimensional EM of theintact heptamer, either assembled from recom-binant proteins or isolated and purified fromyeast cells, revealed an ∼400-A-long Y-shapedarchitecture (93, 94). The reconstitutionof the heptamer from dimeric and trimericpieces uncovered its modular anatomy. Two-dimensional EM of these fragments coupledwith biochemical analyses established therelative positions of its members (Figure 4b).Nup120 is capable of interacting with bothSec13·Nup145C and Seh1·Nup85 (94). All
members of the yeast heptamer are wellconserved; however, the vertebrate complexcontains two additional members, Nup37 andNup43, forming the nonameric Nup107–160complex (64, 96–98). During postmitoticNPC assembly, this complex is recruited tochromatin by MEL-28/ELYS (99). Thus, thisprotein may represent a tenth member of theNup107–160 complex (100). The Nup84 com-plex is localized close to the pore membrane andis suggested to serve as a “membrane-curvingmodule,” similar to the members of the COPI,COPII, and clathrin coats (2, 101). Consistentwith a key structural role of the Nup84 com-plex, deletion or immunodepletion of any of itsmembers has dramatic consequences for the ar-chitecture and function of the NPC, as evidentby the clustering of NPCs in one patch of thenuclear envelope and accumulation of PolyARNA within the nucleus (92, 93, 96, 102–107).
The first crystal structure of a Nup84 com-plex component was the N-terminal domainof human Nup133 (residues 76–478), abbre-viated as hNup13376−478 (throughout the text,the prefixes h, m, and r refer to human, mouse,and rat, respectively; all other proteins are fromyeast. Residue ranges refer to fragments), whichrevealed a seven-bladed β-propeller with twoα-helical insertions and a disordered 3D4Aloop (Figure 4a) (12). This loop was sug-gested to harbor a membrane curvature-sensingmotif termed the ArfGAP1 lipid-packing sen-sor, which forms an amphipathic membranecurvature-sensing α-helix in vitro (108).
The crystal structure of the hNup107658−925·hNup133934−1156 complex shows a compact,
−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−→Figure 4Structural characterization of the heptameric Nup84 complex. The prefix h refers to human; protein nameswithout a prefix refer to yeast. (a) Crystal structures of coat nucleoporins and complexes thereof:hSec13·Nup145C [Protein Data Bank (PDB) codes 3BG1, 3BG0], Seh1·Nup85 (3F3F, 3F3G, 3F3P,3EWE), Nup120NTD (N-terminal domain) (3F7F, 3H7N, 3HXR), Sec13·Nup145C·Nup84NTD (3IKO,3JRO), hNup107CTD·hNup133CTD (C-terminal domain) (3I4R, 3CQC, 3CQG), and hNup133NTD
(1XKS). For those structures with several PDB codes, the first one refers to the displayed structure.(b) Docking of crystal structures into the electron microscopy (EM) envelope of the heptameric Nup84complex ( first panel ). A 90◦-rotated view is shown (second panel ). The EM envelope of the secondreconstructed conformation of the heptamer in which the two hinge regions are completely extended (thirdpanel ). Superposition of the two determined Nup84 conformations ( fourth panel ). The hinge region at theNup145C·Nup84 interface is indicated and was used for the structural alignment.
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hydrophobic interface that is predominantlycomposed of two α-helices of each hNup107and hNup133. Both C-terminal fragmentsform α-helical domains with novel folds (24).
Subsequently, the same hNup107 fragmentwas crystallized in complex with the entireα-helical domain of hNup133 (residues 517–1156) revealing an extended α-helical solenoid
Nup120NTD
hNup133NTD
a
b
90°
Conformation 1 Conformation 2 Superposition
Seh1•Nup85
Sec13
Nup145C
Nup120NTD
Nup84NTD
hNup107CTD
hNup133NTD
hNup133CTD Nup145C•Nup84interface(hinge 1)
Hinge 2
hNup107CTD•hNup133CTD
hNup107CTD
hNup133CTD
hSec13•Nup145C
Nup145C
hSec13
Nup145CDIM
Seh1•Nup85
Nup85
Seh1
Nup85DIM
Sec13•Nup145C•Nup84NTD
Sec13
Nup145C
Nup84NTD
Nup145CDIM
www.annualreviews.org • Nuclear Pore Complex Structure 621
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fold composed of 28 antiparallel α-helices(Figure 4a) (25).
The next advance was the structuraland functional analysis of the hSec131−316·Nup145C125−555 nucleoporin pair (Figure 4a),the centerpiece of the Nup84 complex (8).Sec13 provides six blades to a β-propellerdomain, to which Nup145C contributes anadditional seventh blade to yield a seven-bladed β-propeller. The complementation ofthe β-propeller fold by a domain invasionmotif (DIM) was unprecedented and thus farhas only been observed in complexes con-taining either Sec13 or Seh1 (8, 14, 15,18, 19, 109, 110). The remainder of theNup145C125−555 fragment forms a U-shaped α-helical solenoid domain with a novel fold. Inter-estingly, two different crystal forms harboredidentical hSec131−316·Nup145C125−555 hetero-octameric assemblies that are the result ofhomotypic dimerizations of both hSec131−316
and Nup145C125−555 (Figure 5a). This hetero-octameric assembly can be envisioned to form avertical pole in a cylindrical coat for the nuclearpore membrane (NPC coat) (Figure 5) (8). Insolution, the Sec13·Nup145C pair exists in adynamic equilibrium with various oligomers,including a hetero-octameric species, whichsupports the physiological relevance of the crys-tallized hetero-octamer (8).
Seh1·Nup85, another tightly-associatednucleoporin pair of the heptamer, is ho-mologous to Sec13·Nup145C (8, 94). In-deed, the crystallographic analysis of Seh1·Nup851−570 uncovered a heterodimer that bearsremarkable resemblance to the hSec131−316·Nup145C125−555 pair (Figure 4a) (8, 15).In detail, Seh1·Nup851−570 recapitulates a
seven-bladed β-propeller that is formed by sixblades of Seh1 and complemented by the DIMof Nup85. The α-helical region of Nup85forms a U-shaped α-helical solenoid domainof topology similar to Nup145C. In threedifferent crystal structures, Seh1·Nup851−570
dimerizes into identical heterotetramers that inturn assemble into related, elongated higher-order structures (Figure 5a). Two adjacentSeh1·Nup851−570 tetramers form an elongatedhetero-octamer that closely resembles thehSec131−316·Nup145C125−555 hetero-octamerwith respect to its curvature, symmetry, anddimensions (Figure 5a). This finding suggeststhat this complex forms an additional verticalpole in the proposed NPC coat (8, 15). Com-parison of the higher-order Seh1·Nup851−570
structures in different crystal forms revealsa flexible joint between adjacent heterote-tramers, which may portray conformationalchanges of the pole in the NPC during nucleo-cytoplasmic transport (15). A low-resolutionstructure of Seh1·Nup851−564 obtained froma fourth crystal form confirms the overallarchitecture of two interacting heterodimers(14). However, a conclusive analysis of thisstructure is hampered by the partial characterof the model and the presence of sequenceregister shifts (for details, see Reference 15).
The crystal structure of Nup1201−729
displays a β-propeller and an α-helical domainrepresenting a novel fold with a leucinezipper-like hydrophobic core (Figure 4a) (16,17). The seven-bladed β-propeller domaincontains several insertions, most notably afour-helix bundle, forming a small subdomain.Biochemical analyses uncovered a previouslyunknown interaction of Nup120 with Nup133;
−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−→Figure 5Model for the architecture of a “coat for the nuclear pore membrane.” (a) Structures of the hSec13·Nup145C and Seh1·Nup85hetero-octamers. (b) Binding promiscuity of Nup145C. Nup145C·Nup145C homodimerization in the hSec13·Nup145C hetero-octamer ( panel a, left) and Nup145C·Nup84 heterodimerization in the Sec13·Nup145C·Nup84NTD heterotrimer (right).(c) Schematic representation of the heptameric Nup84 complex and the approximate localization of its seven nucleoporins (left). Eightheptamers are circumferentially arranged in a head-to-tail fashion in four stacked rings, thereby forming a cylindrical scaffold (right).(d ) Two alternative states of the coat for the nuclear pore membrane. Black lines indicate interactions that have not been described aspromiscuous. In one state (left), Nup145C heterodimerizes with Nup84 (red lines). In another state (right), Nup145C homodimerizes(red lines) and forms a vertical hetero-octameric pole. Note that large protein rearrangements would not be necessary to convertbetween the two states.
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~300
Å
Nup84
Nup145C
Nup120
Nup133
Nup85
Sec13
Seh1
Sec13Nup145C
pole
Seh1Nup85
pole
Eightfold
Twofold~400
Å
~1,000 Å
c
Sec13•Nup145C
Seh1•Nup85
Nup120
Nup84•Nup133
a b
hSec13•Nup145Chetero-octamer
Nup145C
hSec13
hSec13
hSec13
hSec13
Nup145C
Nup145C
Nup145C
Seh1•Nup85hetero-octamer
Seh1
Nup85
Seh1
Seh1
Seh1
Nup85
Nup85
Nup85
Nup145C•Nup145Chomodimerization
Nup145C•Nup84heterodimerization
d
Nup84
Nup133
Nup84
Nup133Nup84
Nup133
Nup145C
Sec13Nup120
Nup85
Seh1
Nup84
Nup133Nup84
Nup133
Nup84
Nup133
Nup120Seh1
Nup85
Nup145C
Sec13
Sec13
Nup145C
Sec13
Nup145C
Seh1
Nup85
Nup85
Seh1
Seh1
Nup85
Seh1
Nup85
Sec13
Nup145C
Sec13
Nup145CNup120
Nup120
Nup120
Nup120
1/8 1/8
Nup84
Nup133
Nup145C
Sec13Nup120
Nup85
Seh1
Nup84
Nup133
Nup145C
Sec13Nup120
Nup85
Seh1
Sec13
Nup145C
Sec13
Nup145C
Nup84
Nup133
Nup84
Nup133
Nup84
Nup133
Nup84
Nup133
Nup84
Nup133Nup84
Nup133
Nup84
Nup133
Nup84
Nup133
Seh1
Nup85
Nup145C
Sec13
Sec13
Nup145C
Nup145C
Sec13
Sec13
Nup145C
Seh1
Nup85
Nup85
Seh1
Seh1
Nup85
Nup85
Seh1
Seh1
Nup85
Nup120
Nup120
Nup120 Nup120
Nup120Nup120
Nup145C
Sec13Nup120
Nup85
Seh1
Nup145C
Sec13Nup120
Nup85
Seh1
1/8 1/8
Nup145C•Nup84heterodimerization
Nup145C•Nup145Chomodimerization
90° 90°
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the disruption of this interaction causes asevere mRNA export defect as well as an NPCclustering phenotype in vivo (17). Becausemapping of the individual components in theNup84 complex places Nup120 and Nup133at opposite ends of the heptamer (Figure 5c),these findings are consistent with a head-to-tailarrangement of elongated Nup84 complexes inthe assembled NPC. Interestingly, the attach-ment site for Nup120 lies at the very end of anextended unstructured N-terminal region inNup133 (17). The common occurrence of suchunstructured terminal segments in nucleo-porins (Figure 3) suggests that this anchor-likemechanism of linking two nucleoporins maybe a general feature in the assembled NPC.In cells with open mitosis, these regions maynot only provide flexible tethers betweennucleoporins, but also may be ideal sites forposttranslational modifications, which maytrigger the disassembly of the NPCs (17). Infact, the unstructured segments of the ver-tebrate nonameric Nup107–160 complex arehyperphosphorylated, mainly in N-terminalregions, exclusively during mitosis (65).
The most recent crystallographic ad-vance refers to the structure of theSec13·Nup145C125−555·Nup841−460 complex(Figure 4a) (18). Nup841−460 forms a U-shapedα-helical solenoid domain, topologically simi-lar to two other nucleoporins of the heptamer,Nup145C and Nup85. The interaction be-tween Nup84 and Nup145C is mediated bya hydrophobic interface, located in the kinkregions of the two solenoids, that is reinforcedby additional interactions of two long Nup84loops. The Nup84 binding site partiallyoverlaps with the homodimerization interfaceof Nup145C, suggesting alternative, promis-cuous binding events (Figure 5b). A secondstructure of this complex at significantly lowerresolution corroborates the overall topology,but precludes a detailed analysis owing tosequence register shifts in Nup84 (19).
A 3D EM reconstruction of the Nup84complex at ∼35-A resolution identifies twospecific hinge regions at which the heptamershows great flexibility (Figure 4b) (111). With
the use of tagged proteins, the positioning ofsome of the members was experimentally veri-fied, and the available crystal structures couldbe docked into the maps of the two con-formers (18, 94, 111). Notably, the elongatedZ-shaped Sec13·Nup145C125−555·Nup841−460
heterotrimer was only consistent with one ofthe two heptamer conformers, indicating thatstructural changes occur at the promiscuousNup145C-Nup84 interface (Figures 4b and5b) (18).
The combination of X-ray crystallographicand EM data have yielded an atomic modelfor ∼85% of the Nup84 complex (Figure 4b).The last missing piece of the heptamer per-tains to the triskelion part, which links the threearms of the Y and consists of the C-terminalα-helical regions of Nup120, Nup145C, andNup85 (Figure 3). The structural characteriza-tion of the Nup84 complex serves as a paradigmfor other NPC subcomplexes and illustrates theenormous demand for achieving even higher-resolution EM structures. The relatively sim-ple fold composition and the resulting similarshapes of the building blocks of the heptamersubstantially complicate the docking of crystalstructures into EM maps at current resolutions.
Common Evolutionary Origin of theNuclear Pore Complex and OtherMembrane Coats
According to the “protocoatomer hypothesis”(101), the NPC shares a common evolutionaryorigin with coat protein assemblies (9, 101,112). The recent advances in determiningthe structure of the coat nucleoporins havenot only strengthened this hypothesis butalso unveiled several parallels that extendbeyond the original predictions. Hallmarksof these coat protein complexes are DIMsand topologically similar U-shaped α-helicalsolenoid domains, alternatively termed an-cestral coatomer elements 1 (8, 14, 15, 109).Although the arrangement of coat nucleoporinswithin the NPC is not known at present, theelongated and slightly curved hetero-octamericassemblies of Sec13·Nup145C and
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Seh1·Nup85 bear remarkable similaritiesto the established architecture of Sec13·Sec31in the COPII cage (8, 15, 109, 113, 114). Thebasic repeating unit of the lace-like COPII coatis an elongated Sec13·Sec31 hetero-octamerthat is built from homotypic interactions of theN-terminal β-propeller and the C-terminalα-helical domain of Sec31 (112). Similardesign principles were observed in the recentstructures of Sec13·Sec16, which is thought tobe a template for COPII coat assembly, andof coatomer proteins of the COPI cage (110,115, 116). Notably, pseudoatomic structuresof entire coat cages have only been determinedfor the mammalian clathrin and COPII coatsassembled in vitro (113, 114, 117). By contrast,in vitro assembly systems for the COPI vesiclecoat and the symmetric NPC core havenot been developed thus far, hampering theelucidation of their 3D organization.
Adaptor Nucleoporins: Members ofthe Heteromeric Nic96 Complex
The detailed arrangement of the sevenyeast adaptor nucleoporins Nic96, Nup157,Nup170, Nup188, Nup192, Nup53, andNup59 as well as the overall architecture ofthis subcomplex are not established at present.Structural information of this subcomplex isparticularly relevant for the anatomy of theNPC as the adaptor nucleoporins associate withall other subcomplexes in the symmetric NPCcore. Nup53 and Nup59 engage in interactionswith several other nucleoporins and, hence,appear to be central for this complex. Towardthe pore membrane, Nup53 and Nup59 bindto NDC1 of the transmembrane nucleoporincomplex composed of POM34, POM152, andNDC1 (118–120). Furthermore, Nup53 andNup59 interact with Nup170 and Nup157(120), and the latter weakly binds to the coatnucleoporin Nup120 (95). Nic96 binds tothe large structural nucleoporins Nup188 andNup192 and interacts with Nsp1 of the chan-nel nucleoporins (121–125). The homologousvertebrate Nup93·Nup188·Nup205 complexwas identified in Xenopus oocyte extracts (126).
The human homolog of Nup53 associates withthe Nic96 homolog Nup93 (118). Adaptornucleoporins are primarily α-helical, with onlyNup157 and Nup170 containing a predictedβ-propeller (Figure 3). Nup53 and Nup59differ from other nucleoporins in that they arepredicted to be α/β-proteins that harbor a so-called RNA-recognition motif (RRM) (126).Like the coat nucleoporins, the adaptor nucle-oporins do not contain FG-repeat regions.
The structures of two similar Nic96 frag-ments (Nic96186−839 and Nic96190−839) reveala block-shaped domain that is composed of 32antiparallel α-helices (Figure 6) (22, 23). Con-trary to the regular stacking of the antiparallelhelices in HEAT, Armadillo, or TPR repeatsthat generally result in superhelical solenoids,the α-helices of Nic96 are arranged in anirregular fashion forming a domain with anoverall J-like topology. Strikingly, the Nic96α-helical domain displays a dichotomy of sur-face potentials (23). Whereas the kink regionis highly positively charged, the remainder ofthe domain features a negative electrostatic
Nic96CTD Nup170CTD mNup35 RRM
homodimer
Figure 6Crystal structures of adaptor nucleoporins: Nic96CTD (C-terminal domain)(2RFO, 2QX5), Nup170CTD (3I5P, 3I5Q), and the mNup35 RNA-recognitionmotif (RRM) homodimer (1WWH). The ribbon representations of Nic96CTD
and Nup170CTD are shown in rainbow colors from blue to red along thepolypeptide chain from the N to the C terminus. Protein Data Bank codes arein parentheses. The prefix m refers to mouse; protein names without a prefixrefer to yeast.
www.annualreviews.org • Nuclear Pore Complex Structure 625
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potential, generating a strong dipole moment(23). A C-terminal fragment of Nup170979−1502
also displays an irregular α-helical stack com-posed of 26 α-helices that form an elongatedrod (Figure 6) (25). This domain can bedivided into three segments that remotelyresemble those of the Nup133 α-helicaldomain (Figure 3).
The structure of the RRM in mNup35,the murine homolog of Nup53, displays acharacteristic RRM fold, but noncanonicalribonucleoprotein 1 and 2 motifs, which areresponsible for RNA binding in other RRMdomains (Figure 6) (127, 128). Consistent withthis finding, the RRM domain of mNup35 isunable to bind RNA molecules. Indeed, thepositively charged residues that are typicallyinvolved in RNA binding are mutated to highlyconserved hydrophobic residues that engagein dimer formation, whereas canonical RRMmotifs are monomeric.
Channel Nucleoporins: Members ofthe Heterotrimeric Nsp1 Complex
The innermost cylindrical layer of the NPCscaffold comprises Nsp1, Nup49, and Nup57in yeast (123, 125, 129). These three proteinsshare a similar domain organization in whichan ∼300-residue α-helical region is flanked byFG repeats. The α-helical regions are believedto form the perimeter of the channel, whereasthe tentacle-like FG repeats project into thecentral transport conduit, contributing to thepermeability barrier. Interestingly, Nsp1 is amember of another subcomplex consisting ofthe cytoplasmic filament components Nup82and Nup159 (130, 131). Nsp1 binds to the α-helical region of Nup82 and the N-terminal α-helical region of Nic96 in a promiscuous andmutually exclusive manner (130, 132). The ho-mologous mammalian Nup62 subcomplex con-sists of Nup62, Nup54, Nup58, and the Nup58splice variant Nup45 (133–135).
The only available channel nucleoporinstructure pertains to a portion of the α-helical region of rat Nup58 (Figure 7a) (21).rNup58327−415 forms an α-helical hairpin that
associates in an antiparallel fashion with asecond hairpin via an extensive hydropho-bic interface. In turn, this rNup58327−415
dimer forms distinct tetramers via a polarinterface exclusively featuring large hy-drophilic invariant residues that can functionas hydrogen-bond donors, acceptors, or both.Various rNup58327−415 tetramers display lateraldisplacements of their dimeric building blocksalong the helical axes by up to ∼11 A, corre-sponding to two α-helical turns (Figure 7a).In the different tetramer states, the long sidechains that mediate the dimer-dimer associ-ation engage in remodeled hydrogen-bondnetworks and would act like bristles when the α-helices “slide” against each other. Importantly,the other channel nucleoporins Nup54 andNup62 also contain conserved, amphipathicα-helical regions that may permit their lateraldisplacements. A circular arrangement of thesesliding modules in the fully assembled NPCmay allow the dilation of the central channel inresponse to cargo translocation (Figure 7b,c).Such iris-like adjustments of the central chan-nel have been observed by EM (81, 88, 136).
TRANSPORT FACTORFG-REPEAT INTERACTIONS
The FG-repeat regions of 11 nucleoporins inyeast (Figure 3) form the permeability barrierof the NPC and serve as docking sites forvarious classes of transport receptors. Theinteractions between FG repeats and transportreceptors have been well characterized byX-ray crystallography.
β-Karyopherin FG-RepeatInteractions
β-karyopherins are α-helical proteins that arecomposed of ∼20 HEAT repeats. The ∼40residues of the HEAT motif fold into a pairof antiparallel α-helices that are arranged intandem to form a right-handed superhelicalfold. Cargo recognition by β-karyopherins aswell as their interaction with the small GTPaseRan has been extensively studied (26, 47).
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rNup58/45 state I rNup58/45 state II Superposition
Centralchannel
a
b c
Cargo
Cargo
Cargo
Channelnucleoporins
Figure 7Crystallographic analysis of the channel nucleoporin Nup58. (a) Ribbon representations of two tetramericrat rNup58 conformers (left and middle). Superposition of the two tetrameric rNup58 states (right) reveals alateral shift in which two dimers are offset by up to two helical turns. Note that the crystallized fragmentrefers to a shared region of Nup58 and its splice variant Nup45. (b) Schematic representation of the centralchannel shown along the nucleocytoplasmic axis. Eight rNup58 tetrameric assemblies are circularly arrangedto form a ring (light gray). Simultaneous helical sliding of the eight rNup58 tetramers would result in theoverall dilation of the central channel (dark gray). (c) Localized changes in the channel diameter by α-helicalsliding in response to cargo transport ( purple) across the central channel (orange).
β-karyopherins mediate translocation throughthe NPC via reversible binding to FG repeatsof nucleoporins.
FxFG and GLFG (x denotes any residue) aretwo common core motifs of FG repeats in nu-cleoporins (2). Both motifs were crystallized incomplex with hKap-β11−442 (Figure 8a) (137,138). The FxFG and GLFG motifs intercalateinto the same hydrophobic groove between thehelices of two neighboring HEAT repeats onthe convex surface of the transport receptor.The phenylalanine in the third position of eachmotif is deeply inserted into a hydrophobicpocket and constitutes the predominant bind-ing determinant, thereby providing a structuralbasis for the analogous binding mode of theFxFG and GLFG motifs. A second FxFG motifbinds in a groove adjacent to the primary site.
In both structures, the paucity of the contactsbetween transport factors and FG repeats isconsistent with the observation that their inter-actions are generally of low affinity, reflectingthe need for movement through rather thanstatic binding to the NPC (139). However, theregions between FG repeats can increase theaffinity by forming additional interactions withtransport factors, as illustrated in the structureof Kap95 in complex with a portion of theFG region of Nup1 (Kap95·Nup1963−1076)(140).
Because RanGTP and FG repeats bind todifferent sites on Kap-β1, RanGTP is thoughtto release Kap-β1 from FG nucleoporins byinducing a conformational change (137). Mu-tational and computational analyses suggestthat karyopherins possess significantly more
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hKap-β1•Nsp1FG hTAPUBA•Nsp1FG
a b c d
NTF2•Nsp1FG hTAPp15•hp15•hNup214FG
p15TAP
NTF2 NTF2
Figure 8Crystal structures of transport factors in complex with FG repeats: (a) hKap-β1·Nsp1FG (1F59, 1O6O,1O6P), (b) NTF2·Nsp1FG (1GYB), (c) hTAPp15·hp15·hNup214FG, and (d ) hTAPUBA ·Nsp1FG (1OAI). FGrepeats are illustrated in purple stick representation. Protein Data Bank codes are in parentheses. The prefixh refers to human; protein names without a prefix refer to yeast.
FG-repeat binding sites (up to ∼10) than thosecaptured in the crystal structures (141, 142).Consistent with multiple FG-repeat bindingsites, β-karyopherins are capable of condens-ing FG-repeat regions in single molecule stud-ies, whereas addition of RanGTP restores theirbrush-like extended conformation (36).
RanGDP Import FactorNTF2-FG-Repeat Interactions
Nuclear export is mediated by heterotrimericcomplexes composed of cargo, export Kap-β,and RanGTP, which are dismantled by RanGTPase-activating proteins (RanGAPs) on thecytoplasmic face of the NPC (SupplementalMovie 2) (143). To replenish RanGTP de-pleted in the nucleus during export, RanGDPis reimported by nuclear transport factor2 (NTF2, also known as p10) (144–146).NTF2 forms a homodimer with two RanGDPbinding sites at opposite ends of the dimerand two binding sites for FG repeats at thedimer interface (Figure 8b) (147, 148). NTF2recapitulates the FxFG recognition of Kap-βin which the second phenylalanine in an overallsimilar conformation is deeply buried in ahydrophobic pocket (137, 147).
mRNA Export FactorTAP-p15-FG-Repeat Interactions
The export of mRNA into the cytosol oc-curs independently of Ran and karyopherins,and instead, it is mediated by a dedicated het-erodimeric mRNA export factor composed ofTAP and p15 in metazoans (Mex67 and Mtr2 inyeast). TAP comprises four domains arrangedin tandem: an N-terminal RNA-binding do-main, followed by a leucine-rich repeat do-main, a p15-binding domain, and a C-terminalubiquitin-associated (UBA) domain. Both theRNA-binding and leucine-rich repeat domainsare required for RNA cargo binding, whereasthe two C-terminal domains facilitate the asso-ciation with FG repeats.
The structure of the p15-binding domain ofTAP in complex with p15 and an FG-repeat re-gion of hNup214 closely resembles the NTF2homodimer, but unveiled only one FG-repeatbinding site located on TAP (Figure 8c) (149).Again, the second phenylalanine is bound in ahydrophobic pocket, and the peptide backboneassumes a conformation that is similar to theKap-β-bound FxFG motif. The p15-bindingdomain of TAP exclusively recognizes the FGmoiety (149), whereas the helical bundle of theC-terminal UBA domain intimately interacts
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with both aromatic residues of an Nsp1 FxFGcore region (Figure 8d ) (150).
STRUCTURES OF ASYMMETRICNUCLEOPORINS
The symmetric core of the NPC is decoratedwith cytoplasmic filaments and a nuclear basketstructure that are built from different setsof nucleoporins (Figures 1 and 2). Theseasymmetric nucleoporins are key componentsin establishing the directionality of nucleo-cytoplasmic transport. Several asymmetricnucleoporins contain FG repeats that serve asbinding sites for karyopherins. Altogether, ∼14proteins can be considered to be asymmetricnucleoporins (Figure 2).
Cytoplasmic Filament Nucleoporinsand Associated mRNA Export Factors
The yeast cytoplasmic filaments are primarilycomposed of Nup82 and Nup159 and providebinding sites for various mRNA export factorsthat are critical for mRNA ribonucleoproteinremodeling events. Because mRNA export fac-tors are constitutively attached to the cytoplas-mic filaments, they can be considered part of theNPC. The DEAD-box helicase Dbp5 (hDbp5)plays a central role in the remodeling machin-ery and is recruited to the NPC via Nup159(hNup214). The ATPase activity of Dbp5 isstimulated by Gle1 (hGle1) and the smallcoactivator molecule inositol hexakisphosphate(151, 152). Gle1 is recruited to the cytoplasmicface of the NPC via its interaction with Nup42.
The structure of Nup1591−387 reveals an un-usually asymmetric seven-bladed β-propeller(Figure 9a) (11). The structure of the corre-sponding domain of hNup214 (residues 1–450)is similar in its conserved asymmetric core butdeviates from its yeast counterpart by numerousextended loops and a ∼30-residue C-terminalpeptide segment, which folds back onto theβ-propeller and binds to its bottom face(Figure 9b) (13). The complex ofhNup2141−450 with hDbp5-ADP showsthat the association between the two proteins
is primarily mediated by the 6D7A loop ofthe β-propeller and the N-terminal RecA-likedomain of hDbp5 (Figure 9c) (153, 154).Strikingly, the interface is characterized bystrong opposing electrostatic surface poten-tials. The positively charged surface area ofhDbp5 that binds hNup214 is also utilizedfor its interaction with RNA, as visualizedin the structure of hDbp5 in complex withthe ATP analog AMPPNP and U6-RNA(Figure 9d ) (154, 155). These findings explainthe mutually exclusive binding events. Whereasthe N-terminal RecA-like domain of hDbp5interacts with hNup214, the C-terminal RecA-like domain binds the ATPase activator Gle1(156). The relative arrangement of the twoRecA-like domains is governed by the boundnucleotide (Figure 9e) (155). Altogether,the conformational changes and the iterativeswitch in binding partners of hDbp5 have beenproposed to be an integral part of a ratchetmechanism of mRNA export (42, 153, 154).
Nup145N (hNup98) is another mRNAexport factor, which localizes to the cytoplas-mic filaments via its interaction with Nup82.Nup145N and Nup145C (hNup96) are theN-terminal and C-terminal products of theevolutionarily conserved autoproteolytic cleav-age of the Nup145 (hNup98–96) precursorprotein, which is catalyzed by the C-terminaldomain of Nup145N (97, 157). Nup145C ispart of the Nup84 complex (92). The structureof hNup98676−920 reveals a novel α/β-fold andprovides mechanistic insight into the autopro-teolytic cleavage (Figure 9f ) (158–160). In ad-dition to catalysis, the autoproteolytic domainof hNup98 is responsible for its NPC localiza-tion. hNup98 is homologous to three proteinsin yeast, Nup145N, Nup100, and Nup116,which share a similar domain organization (161,162). Although Nup100 and Nup116 possessthe autoproteolytic domain, these nucleoporinsare not generated by autoproteolysis.
The autoproteolytic domain is predictedto be the only structured region of hNup98,whereas the remaining ∼700-residue re-gion contains numerous FG repeats and the57-residue Gle2-binding sequence (GLEBS,
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hNup214NTD hNup214NTD•hDbp5-ADP
hNup98APD•hNup96N
Nup98APD
Nup96N peptide
Nup159NTD
hDbp5-AMPPNP•U6-RNA
Rae1
Nup98GLEBS
hRae1•hNup98GLEBS
a
α-helical region1 830 1,301 1,848 2,142 2,439 2,771 3,040 3,224
I Zinc fingers II III E3 IV CycH1,171 1,355 2,012 2,309 2,631 2,911 3,062
j
b c
d e f
g
hDbp5-ADP
hSUMO•hRanGAP1CTD•hUbc9•hNup358E3
RanGAP1CTD
Ubc9
Nup358E3
Sumo
i
hRan-GMPPNP•hNup358RanBD1
Ran Nup358RanBD1
h
Figure 9Crystal structures of cytoplasmic-filament nucleoporins and associated mRNA export factors:(a) Nup159NTD (1XIP), (b) hNup214NTD (2OIT), (c) hNup214NTD·hDbp5-ADP (3FMO, 3FMP, 3FHC),(d ) hDbp5-AMPPNP·U6-RNA (3FHT, 3G0H), (e) hDbp5-ADP (3EWS), ( f ) hNup98APD·hNup96N
(1KO6), ( g) hRae1·hNup98GLEBS (3MMY), (h) hRan-GMPPNP·hNup358RanBD1 (1RRP), (i ) hSUMO·hRanGAP1CTD·hUbc9·hNup358E3 (1Z5S), and ( j) domain organization of hNup358. APD, autoproteolyticdomain; CycH, cyclophilin homology domain; CTD, C-terminal domain; E3, E3 ligase domain; GLEBS,Gle2-binding sequence; I−IV, Ran-binding domains; NTD, N-terminial domain; RanBD, Ran-bindingdomain. Protein Data Bank codes are in parentheses. The prefix h refers to human; protein names without aprefix refer to yeast.
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residues 157–213), which serves as the dock-ing site for the human mRNA export factorhRae1 (Gle2 in yeast) (Figure 3). This inter-action is essential for a normal morphologyof the NPC with respect to the surroundingouter nuclear envelope membrane. Among thethree yeast hNup98 homologs, only Nup116features a GLEBS motif. The structure ofhRae1·hNup98GLEBS reveals a seven-bladed β-propeller of hRae1 with several extensive sur-face loops that binds the GLEBS motif on itstop face (Figure 9g) (20).
Vertebrates contain an additional cyto-plasmic filament nucleoporin, Nup358, whichprovides binding sites for transport factors,Ran, and RanGAP1. These binding eventsplay important roles in the assembly anddisassembly of karyopherin-cargo transportcomplexes (163, 164). Nup358 contains four∼150-residue domains that facilitate binding toRan (RanBD1–4) (Figure 9j). The structuralanalysis of Ran bound to the nonhydrolysableGTP analog GMPPNP in complex withhNup358RanBD1 reveals that the GTPasedomain of Ran and its tethered C-terminalhelix embrace the pleckstrin-homology do-main of hNup358RanBD1 (Figure 9h) (165). A63-residue region in hNup358 provides thebinding site for SUMOylated RanGAP1 andwas visualized in the structure of the hSUMO·hRanGAP1419−587·hUbc9·hNup3582631−2693
complex (Figure 9i) (166).
Nuclear Basket Nucleoporins
The nuclear basket represents the least ex-plored part of the NPC and is composed ofNup1, Nup2, Nup60, Mlp1, and Mlp2 in yeast,whereas the vertebrate basket harbors onlythree nucleoporins, Nup153, Nup50, and TPR.In addition to the large coiled-coils of Mlp1/2(TPR), the nuclear basket nucleoporins con-tain α/β-regions and FG repeats (Figure 3).Furthermore, Nup153 contains four zinc fin-gers arranged in tandem that are not presentin its yeast homolog Nup1 and that facilitatebinding to Ran in both its GDP- and GTP-bound states. Notably, eight zinc fingers are
also present in Nup358. Together, the zinc fin-ger domains of these two nucleoporins appearto generate a high local Ran concentration atthe NPC, increasing the efficiency of nucleo-cytoplasmic transport (167).
The structural analyses of individualrNup153 zinc finger motifs in complex withhRan-GDP demonstrate that each zinc fingermodule independently binds to Ran in anidentical fashion (Figure 10) (168–170).Another important function of the nuclearbasket is the termination of Kap-α-mediatedcargo import. The structures of Kap-α boundto nuclear localization sequence peptides orin complex with a short N-terminal sequencemotif of mNup50 (Nup2) show that the sameKap-α surface is utilized for both bindingevents, thereby providing a structural basisfor basket-mediated disassembly of importcomplexes (Figure 10) (171–173).
MODELS OF THE SYMMETRICNUCLEAR PORE COMPLEX CORE
The highest resolution of EM reconstructionsof the entire NPC obtained to date (∼60 A)does not allow the placement of individualcrystal structures (51, 89). Even the dockingof the entire ∼400-A-long Nup84 complex,which represents a major portion of the sym-metric NPC core, determined to ∼35-A res-olution has not yet been achieved. Therefore,the spatial arrangement and stoichiometry ofthe nucleoporins in the NPC core remain un-known. Moreover, neighboring nucleoporinswithin the intact NPC may potentially mod-ulate the interactions that are observed in 3DEM reconstructions of the isolated heptamerand in the crystal structures. Further compli-cating factors in the structural characterizationof the NPC are its flexible nature and dynamicchanges, such as the dilation of the central chan-nel during transport or the proposed lateralopening of the NPC scaffold during the importof integral membrane proteins (Figure 3c,d andMovies 3 and 4) (21, 88, 112, 136). An attractivescenario to explain this remarkable plasticitywould be the notion that nucleoporins change
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rNup153ZnF2•hRanGDP
Nup153ZnF2
RanGDP
mKap-α•mNup50N
Kap-α
Nup50N
646 876
C1,683
Zinc fingersUnstructured FG repeatsNup153 N1
a
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Zn2+
Mg2+
Figure 10(a) Crystal structures of basket nucleoporins: mKap-α·mNup50N (2C1M) and rNup153ZnF2·hRanGDP (3CH5, 3GJ3–8). The Zn andMg ions are represented as orange and red spheres, respectively. (b) Domain organization of hNup153. The red bar marks the fragmentwhose crystal structure is experimentally determined. Protein Data Bank codes are in parentheses. N, N-terminal domain; h, human;m, mouse; r, rat.
their interaction partners dynamically. In thisrespect, the symmetric NPC core can be re-garded to possess fluid-like properties. Supportfor this idea comes from crystal structures thatreveal promiscuous interactions (8, 18, 19, 21).Collectively, these considerations illustrate thedifficulty in arriving at a high-resolution struc-ture of the intact NPC. In the absence of high-resolution EM structures of the intact NPC,alternative indirect approaches have thereforebeen applied to formulate models for the archi-tecture of the NPC.
We proposed a model termed “coat for thenuclear pore membrane,” or “NPC coat,” thatwas deduced from several crystal structures,biochemical and in vivo analyses, homologiesbetween COPII components and nucleoporins,
as well as symmetry and size considerationsderived from EM studies (Figure 5c) (8, 15,112). Specifically, we made the assumption thatthe arrangement of the seven nucleoporins ofthe heptameric Nup84 complex corresponds totheir mapped positions in the isolated heptamerand that the observed hetero-octameric as-semblies of Sec13·Nup145C and Seh1·Nup85occur as vertical poles in the assembled NPC.These assumptions would result in a cylindricalscaffold that positions 32 copies of each of theseven nucleoporins in four rings, which arestacked in an antiparallel fashion, consistentwith the eight- and twofold rotational symme-tries of the NPC core. The overall dimensionsof this cylindrical NPC coat would be in accordwith the experimentally determined size of
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the yeast NPC (Figure 5c). The observedpromiscuity of Nup145C to interact witheither Nup145C or Nup84 suggests that alter-native interactions can occur, whereas othertight interactions, such as those within theSec13·Nup145C and Seh1·Nup85 pairs, arenot expected to break. In summary, the proteinswould maintain their relative position in thescaffold, whereas changes in their interactionpartners would confer a dynamic character tothe NPC (Figure 5d ). This NPC coat is envi-sioned to be sandwiched between the POM andthe adaptor cylinders and to contain gaps andholes, which would allow for interdigitationwith adjacent nucleoporins (Figure 1b).
In an alternative “computational model,” adiverse set of biophysical and proteomic data
was used as input to calculate a blueprint ofthe NPC (Figure 11a) (67, 174). Key assump-tions of this model refer to a fixed absolute stoi-chiometry of 30 different nucleoporins (456proteins in total), to a static single state of theNPC, and to the symmetry of the NPC estab-lished by EM. In the resulting model, Nup84complexes would form two separated rings onthe cytoplasmic and nucleoplasmic periphery,each containing eight copies of the heptamer.These peripheral outer rings would sandwichtwo inner rings containing Nup157, Nup170,Nup188, and Nup192. Attached onto this scaf-fold are the remaining nucleoporins.
The third model resembles the computa-tional model in that it contains two periph-eral outer rings each containing eight copies of
Cytoplasmicring
Inner ring
Nucleoplasmicring
b
aOuter rings Inner rings Symmetric NPC core
Nup133
Nup120
Nup
84
Nup85
Nup1
45C
Sec13
Seh1
Figure 11Alternative models of the architecture of the symmetric nuclear pore complex (NPC) core. (a) The “computational model” and (b) the“lattice model.” For details, see description in the text. Images are reprinted with permission from References 67 and 14, respectively.
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the heptameric Nup84 complex, but this modeldiffers in that it features only a single innerring composed of Nic96, Nup157, Nup170,Nup188, and Nup192 (Figure 11b) (14). Thekey difference from the other two models isthe assumption that the Nup84 complexes arenot arranged horizontally but vertically, withNup133 molecules facing toward the nucle-oplasm and cytoplasm, respectively. The fiveproteins of the inner ring are assumed to assem-ble into a structural unit that would bridge thetips of the Y-shaped heptamers at the equato-rial plane in a lattice-like fashion. Since the firstintroduction of the “lattice model,” four strik-ingly different arrangements were proposed forthis lattice (14, 175, 176).
Owing to the assumptions and uncertain-ties, the proposed models clearly have to beconsidered as working hypotheses that provide
an important framework for future experimentsand validations. The determination of the re-maining individual nucleoporin structures inthe near future will certainly help to improveand potentially modify the current modelsand continue to provide unexpected and spec-tacular insight into the complex architectureof the NPC. However, the greatest advancestoward an atomic structure of the NPC willprobably be the structure determinations oflarge multinucleoporin complexes by X-raycrystallography and/or EM. The challenge isthen to assemble an atomic-resolution mosaicof the entire NPC. With the rapid pace ofthe past five years, we are optimistic that thisgreat challenge will be overcome, resultingin the elucidation of the remaining mysteriesof the NPC, one of the largest proteinaceousassemblies of the eukaryotic cell.
SUMMARY POINTS
1. The nuclear pore complex (NPC) is embedded in pores of the nuclear envelope andconstitutes the portal for all transport events between the cytoplasm and the nucleus.The NPC consists of an evolutionarily conserved set of ∼30 different proteins, termednucleoporins, that are organized into several subcomplexes, each of which occurs inmultiple copies, resulting in ∼500–1,000 protein molecules in the fully assembled NPC.
2. The characterization of the NPC by electron microscopy (EM) revealed a doughnut-shaped central core with eightfold rotational symmetry that is decorated with cytoplasmicfilaments and a nuclear basket. The NPC is flexible and dynamic, as, for example, observedduring cargo translocation.
3. The permeability barrier of the NPC is formed by unstructured phenylalanine-glycine(FG)-repeat regions that also serve as docking sites for transport factor-cargo complexes.Whereas the mobile transport machinery is reasonably well understood at the atomiclevel, the precise nature of the permeability barrier remains an area of heavy debate.
4. The large size, flexible nature, and difficulty of obtaining sufficient quantities of puri-fied NPCs preclude the structure determination of the entire NPC with present X-raycrystallography technology. Therefore, a divide-and-conquer strategy has been applied,whereby crystal structures of NPC components are determined and then assembled intohigher-order structures with the help of EM and computational approaches.
5. The predominant folds present in nucleoporins are seven-bladed β-propellers and ir-regular α-helical zigzag domains. Surprisingly, two seven-bladed β-propellers contain ablade that is contributed in trans by another nucleoporin, an architectural feature that isalso observed in the COPII vesicle coat.
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6. The crystal structures of the components of the heptameric Nup84 complex could ap-proximately be fit into a 3D EM map of the entire heptamer. The Nup84 complexdisplays conformational flexibility, and some of its components can interact in a promis-cuous fashion, which perhaps provides a structural basis for the flexible nature of theNPC.
7. The structures of NPC components and of coat protein complexes in the endocytic andsecretory pathways uncovered striking similarities with respect to their folds, architec-tures, and associations, supporting their common evolutionary origin in a progenitorprotocoatomer.
8. Various architectures for the symmetric NPC core have been proposed on the basis ofdifferent approaches and assumptions that need to be validated in the future. Therefore,these models should be regarded as working hypotheses.
FUTURE ISSUES
1. The remaining structured regions of nucleoporins and further subcomplexes are expectedto be determined in the near future. Specifically, the heteromeric Nic96 complex needsto be characterized in a similar fashion as the heptameric Nup84 complex.
2. The current highest resolution of EM reconstructions of the entire NPC is insufficientfor the docking of nucleoporin crystal structures. Pushing this resolution limit throughsignificant advances in EM techniques and a complete inventory of nucleoporin structuresmay ultimately yield a complete pseudoatomic model for the entire NPC and resolvemajor unresolved questions, such as its detailed architecture and stoichiometry.
3. The following key questions must be addressed: What is the stoichiometry of the ∼30nucleoporins in the assembled NPC? What is the basis for the substantial mass differencebetween vertebrate and yeast NPCs (∼112 versus ∼66 MDa)? Do nucleoporins interactwith each other in the assembled NPC in the same way as in isolated subcomplexes?
4. Can the structure of the NPC be assembled in a LEGO-like fashion from its individualparts? What is the molecular mechanism for the cell cycle–dependent reversible assemblyand disassembly in cells with open mitosis? Are there cellular factors that regulate theassembly and/or disassembly of the NPC? The development of an in vitro assemblysystem of the symmetric NPC core would certainly help in answering these questions.
5. Transport events such as the import of integral membrane proteins of the nuclear enve-lope destined for the inner nuclear membrane suggest that large-scale rearrangementsoccur in the NPC. However, the structural basis and molecular mechanisms are poorlyunderstood.
6. The promiscuous nature of the NPC complicates the in vivo analysis with current func-tional assays. An additional obstacle is the fact that nucleoporins have distinct functionsduring the cell cycle. Therefore, in vitro assays that quantitatively probe the NPC func-tion need to be developed.
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7. The ultimate goal of the structural characterization of the NPC is an atomic-resolutionmovie that depicts the dynamic changes of the NPC during nucleocytoplasmic transportof various cargoes and that integrates the many other functions of the NPC.
8. The advances in the structural characterization of the NPC will finally contribute to abetter understanding of the mechanisms of “nucleoporin diseases,” which in many casesremain enigmatic at present.
DISCLOSURE STATEMENT
The authors are not aware of any affiliations, memberships, funding, or financial holdings thatmight be perceived as affecting the objectivity of this review.
ACKNOWLEDGMENTS
We thank Kuo-Chiang Hsia, Jana Mitchell, Vivien Nagy, Alina Patke, Tobias Reichenbach, Hyuk-Soo Seo, Pete Stavropoulos, and Deniz Top for discussions and comments on the manuscript, andStephanie Etherton for help with editing the manuscript. E.W.D. is the Dale F. and Betty AnnFrey Fellow of the Damon Runyon Cancer Research Foundation, DRG-1977-08, and A.H. wassupported by a SCOR grant from the Leukemia and Lymphoma Society and by a V Scholar Awardfrom the V Foundation for Cancer Research. We apologize in advance to those investigators whosework was inadvertently overlooked or could not be included due to space restrictions.
LITERATURE CITED
1. Davis LI, Blobel G. 1986. Identification and characterization of a nuclear pore complex protein. Cell45:699–709
2. Rout MP, Aitchison JD, Suprapto A, Hjertaas K, Zhao Y, Chait BT. 2000. The yeast nuclear porecomplex: composition, architecture, and transport mechanism. J. Cell Biol. 148:635–51
3. Cronshaw JM, Krutchinsky AN, Zhang W, Chait BT, Matunis MJ. 2002. Proteomic analysis of themammalian nuclear pore complex. J. Cell Biol. 158:915–27
4. DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, et al. 2009. Evidence for a shared nuclear porecomplex architecture that is conserved from the last common eukaryotic ancestor. Mol. Cell. Proteomics8:2119–30
5. Rout MP, Blobel G. 1993. Isolation of the yeast nuclear pore complex. J. Cell Biol. 123:771–836. Reichelt R, Holzenburg A, Buhle EL Jr, Jarnik M, Engel A, Aebi U. 1990. Correlation between structure
and mass distribution of the nuclear pore complex and of distinct pore complex components. J. Cell Biol.110:883–94
7. Rabut G, Doye V, Ellenberg J. 2004. Mapping the dynamic organization of the nuclear pore complexinside single living cells. Nat. Cell Biol. 6:1114–21
8. Hsia KC, Stavropoulos P, Blobel G, Hoelz A. 2007. Architecture of a coat for the nuclear pore membrane.Cell 131:1313–26
9. Devos D, Dokudovskaya S, Williams R, Alber F, Eswar N, et al. 2006. Simple fold composition andmodular architecture of the nuclear pore complex. Proc. Natl. Acad. Sci. USA 103:2172–77
10. Paoli M. 2001. Protein folds propelled by diversity. Prog. Biophys. Mol. Biol. 76:103–3011. Weirich CS, Erzberger JP, Berger JM, Weis K. 2004. The N-terminal domain of Nup159 forms a beta-
propeller that functions in mRNA export by tethering the helicase Dbp5 to the nuclear pore. Mol. Cell16:749–60
636 Hoelz · Debler · Blobel
Ann
u. R
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011.
80:6
13-6
43. D
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d fr
om w
ww
.ann
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ws.
org
by M
arsh
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nive
rsity
on
11/2
8/11
. For
per
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l use
onl
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BI80CH26-Hoelz ARI 16 May 2011 12:36
12. Berke IC, Boehmer T, Blobel G, Schwartz TU. 2004. Structural and functional analysis of Nup133domains reveals modular building blocks of the nuclear pore complex. J. Cell Biol. 167:591–97
13. Napetschnig J, Blobel G, Hoelz A. 2007. Crystal structure of the N-terminal domain of the humanprotooncogene Nup214/CAN. Proc. Natl. Acad. Sci. USA 104:1783–88
14. Brohawn SG, Leksa NC, Spear ED, Rajashankar KR, Schwartz TU. 2008. Structural evidence forcommon ancestry of the nuclear pore complex and vesicle coats. Science 322:1369–73
15. Debler EW, Ma Y, Seo HS, Hsia KC, Noriega TR, et al. 2008. A fence-like coat for the nuclear poremembrane. Mol. Cell 32:815–26
16. Leksa NC, Brohawn SG, Schwartz TU. 2009. The structure of the scaffold nucleoporin Nup120 revealsa new and unexpected domain architecture. Structure 17:1082–91
17. Seo HS, Ma Y, Debler EW, Wacker D, Kutik S, et al. 2009. Structural and functional analysis of Nup120suggests ring formation of the Nup84 complex. Proc. Natl. Acad. Sci. USA 106:14281–86
18. Nagy V, Hsia KC, Debler EW, Kampmann M, Davenport AM, et al. 2009. Structure of a trimericnucleoporin complex reveals alternate oligomerization states. Proc. Natl. Acad. Sci. USA 106:17693–98
19. Brohawn SG, Schwartz TU. 2009. Molecular architecture of the Nup84-Nup145C-Sec13 edge elementin the nuclear pore complex lattice. Nat. Struct. Mol. Biol. 16:1173–77
20. Ren Y, Seo HS, Blobel G, Hoelz A. 2010. Structural and functional analysis of the interaction betweenthe nucleoporin Nup98 and the mRNA export factor Rae1. Proc. Natl. Acad. Sci. USA 107:10406–11
21. Melcak I, Hoelz A, Blobel G. 2007. Structure of Nup58/45 suggests flexible nuclear pore diameter byintermolecular sliding. Science 315:1729–32
22. Jeudy S, Schwartz TU. 2007. Crystal structure of nucleoporin Nic96 reveals a novel, intricate helicaldomain architecture. J. Biol. Chem. 282:34904–12
23. Schrader N, Stelter P, Flemming D, Kunze R, Hurt E, Vetter IR. 2008. Structural basis of the nic96subcomplex organization in the nuclear pore channel. Mol. Cell 29:46–55
24. Boehmer T, Jeudy S, Berke IC, Schwartz TU. 2008. Structural and functional studies of Nup107/Nup133interaction and its implications for the architecture of the nuclear pore complex. Mol. Cell 30:721–31
25. Whittle JR, Schwartz TU. 2009. Architectural nucleoporins Nup157/170 and Nup133 are structurallyrelated and descend from a second ancestral element. J. Biol. Chem. 284:28442–52
26. Cook A, Bono F, Jinek M, Conti E. 2007. Structural biology of nucleocytoplasmic transport. Annu. Rev.Biochem. 76:647–71
27. Chook YM, Blobel G. 2001. Karyopherins and nuclear import. Curr. Opin. Struct. Biol. 11:703–1528. Feldherr CM. 1962. The nuclear annuli as pathways for nucleocytoplasmic exchanges. J. Cell Biol. 14:65–
7229. Paine PL, Moore LC, Horowitz SB. 1975. Nuclear envelope permeability. Nature 254:109–1430. Pante N, Kann M. 2002. Nuclear pore complex is able to transport macromolecules with diameters of
about 39 nm. Mol. Biol. Cell 13:425–3431. Macara IG. 2001. Transport into and out of the nucleus. Microbiol. Mol. Biol. Rev. 65:570–9432. Rout MP, Aitchison JD, Magnasco MO, Chait BT. 2003. Virtual gating and nuclear transport: the hole
picture. Trends Cell Biol. 13:622–2833. Shulga N, Goldfarb DS. 2003. Binding dynamics of structural nucleoporins govern nuclear pore complex
permeability and may mediate channel gating. Mol. Cell. Biol. 23:534–4234. Strawn LA, Shen T, Shulga N, Goldfarb DS, Wente SR. 2004. Minimal nuclear pore complexes define
FG repeat domains essential for transport. Nat. Cell Biol. 6:197–20635. Frey S, Richter RP, Gorlich D. 2006. FG-rich repeats of nuclear pore proteins form a three-dimensional
meshwork with hydrogel-like properties. Science 314:815–1736. Lim RY, Fahrenkrog B, Koser J, Schwarz-Herion K, Deng J, Aebi U. 2007. Nanomechanical basis of
selective gating by the nuclear pore complex. Science 318:640–4337. Naim B, Zbaida D, Dagan S, Kapon R, Reich Z. 2009. Cargo surface hydrophobicity is sufficient to
overcome the nuclear pore complex selectivity barrier. EMBO J. 28:2697–70538. Miao L, Schulten K. 2010. Probing a structural model of the nuclear pore complex channel through
molecular dynamics. Biophys. J. 98:1658–67
www.annualreviews.org • Nuclear Pore Complex Structure 637
Ann
u. R
ev. B
ioch
em. 2
011.
80:6
13-6
43. D
ownl
oade
d fr
om w
ww
.ann
ualr
evie
ws.
org
by M
arsh
all U
nive
rsity
on
11/2
8/11
. For
per
sona
l use
onl
y.
BI80CH26-Hoelz ARI 16 May 2011 12:36
39. Yamada J, Phillips JL, Patel S, Goldfien G, Calestagne-Morelli A, et al. 2010. A bimodal distribution oftwo distinct categories of intrinsically-disordered structures with separate functions in FG nucleoporins.Mol. Cell. Proteomics 9:2205–24
40. Hoelz A, Blobel G. 2004. Cell biology: popping out of the nucleus. Nature 432:815–1641. Pemberton LF, Paschal BM. 2005. Mechanisms of receptor-mediated nuclear import and nuclear export.
Traffic 6:187–9842. Stewart M. 2007. Ratcheting mRNA out of the nucleus. Mol. Cell 25:327–3043. Stewart M. 2007. Molecular mechanism of the nuclear protein import cycle. Nat. Rev. Mol. Cell Biol.
8:195–20844. Kohler A, Hurt E. 2007. Exporting RNA from the nucleus to the cytoplasm. Nat. Rev. Mol. Cell Biol.
8:761–7345. Debler EW, Blobel G, Hoelz A. 2009. Nuclear transport comes full circle. Nat. Struct. Mol. Biol. 16:457–
5946. Stewart M. 2009. Cell biology. Nuclear export of small RNAs. Science 326:1195–9647. Cook AG, Conti E. 2010. Nuclear export complexes in the frame. Curr. Opin. Struct. Biol. 20:247–5248. Kiseleva E, Goldberg MW, Allen TD, Akey CW. 1998. Active nuclear pore complexes in Chironomus:
visualization of transporter configurations related to mRNP export. J. Cell Sci. 111:223–3649. King MC, Lusk CP, Blobel G. 2006. Karyopherin-mediated import of integral inner nuclear membrane
proteins. Nature 442:1003–750. Saksena S, Summers MD, Burks JK, Johnson AE, Braunagel SC. 2006. Importin-alpha-16 is a translocon-
associated protein involved in sorting membrane proteins to the nuclear envelope. Nat. Struct. Mol. Biol.13:500–8
51. Beck M, Lucic V, Forster F, Baumeister W, Medalia O. 2007. Snapshots of nuclear pore complexes inaction captured by cryo-electron tomography. Nature 449:611–15
52. Blobel G. 1985. Gene gating: a hypothesis. Proc. Natl. Acad. Sci. USA 82:8527–2953. Galy V, Olivo-Marin JC, Scherthan H, Doye V, Rascalou N, Nehrbass U. 2000. Nuclear pore complexes
in the organization of silent telomeric chromatin. Nature 403:108–1254. Feuerbach F, Galy V, Trelles-Sticken E, Fromont-Racine M, Jacquier A, et al. 2002. Nuclear architecture
and spatial positioning help establish transcriptional states of telomeres in yeast. Nat. Cell Biol. 4:214–2155. Fahrenkrog B, Koser J, Aebi U. 2004. The nuclear pore complex: a jack of all trades? Trends Biochem.
Sci. 29:175–8256. Akhtar A, Gasser SM. 2007. The nuclear envelope and transcriptional control. Nat. Rev. Genet. 8:507–1757. Nagai S, Dubrana K, Tsai-Pflugfelder M, Davidson MB, Roberts TM, et al. 2008. Functional targeting
of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase. Science 322:597–60258. Khadaroo B, Teixeira MT, Luciano P, Eckert-Boulet N, Germann SM, et al. 2009. The DNA damage
response at eroded telomeres and tethering to the nuclear pore complex. Nat. Cell Biol. 11:980–8759. Towbin BD, Meister P, Gasser SM. 2009. The nuclear envelope—a scaffold for silencing? Curr. Opin.
Genet. Dev. 19:180–8660. Capelson M, Liang Y, Schulte R, Mair W, Wagner U, Hetzer MW. 2010. Chromatin-bound nuclear
pore components regulate gene expression in higher eukaryotes. Cell 140:372–8361. Strambio-de-Castillia C, Niepel M, Rout MP. 2010. The nuclear pore complex: bridging nuclear trans-
port and gene regulation. Nat. Rev. Mol. Cell Biol. 11:490–50162. Wozniak R, Burke B, Doye V. 2010. Nuclear transport and the mitotic apparatus: an evolving relation-
ship. Cell. Mol. Life Sci. 67:2215–3063. Belgareh N, Rabut G, Bai SW, van Overbeek M, Beaudouin J, et al. 2001. An evolutionarily conserved
NPC subcomplex, which redistributes in part to kinetochores in mammalian cells. J. Cell Biol. 154:1147–60
64. Loıodice I, Alves A, Rabut G, Van Overbeek M, Ellenberg J, et al. 2004. The entire Nup107–160complex, including three new members, is targeted as one entity to kinetochores in mitosis. Mol. Biol.Cell 15:3333–44
65. Glavy JS, Krutchinsky AN, Cristea IM, Berke IC, Boehmer T, et al. 2007. Cell-cycle-dependent phos-phorylation of the nuclear pore Nup107–160 subcomplex. Proc. Natl. Acad. Sci. USA 104:3811–16
638 Hoelz · Debler · Blobel
Ann
u. R
ev. B
ioch
em. 2
011.
80:6
13-6
43. D
ownl
oade
d fr
om w
ww
.ann
ualr
evie
ws.
org
by M
arsh
all U
nive
rsity
on
11/2
8/11
. For
per
sona
l use
onl
y.
BI80CH26-Hoelz ARI 16 May 2011 12:36
66. Suntharalingam M, Wente SR. 2003. Peering through the pore: nuclear pore complex structure, assem-bly, and function. Dev. Cell 4:775–89
67. Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, et al. 2007. The molecular architecture ofthe nuclear pore complex. Nature 450:695–701
68. Orjalo AV, Arnaoutov A, Shen Z, Boyarchuk Y, Zeitlin SG, et al. 2006. The Nup107–160 nucleoporincomplex is required for correct bipolar spindle assembly. Mol. Biol. Cell 17:3806–18
69. Zuccolo M, Alves A, Galy V, Bolhy S, Formstecher E, et al. 2007. The human Nup107–160 nuclearpore subcomplex contributes to proper kinetochore functions. EMBO J. 26:1853–64
70. Mishra RK, Chakraborty P, Arnaoutov A, Fontoura BM, Dasso M. 2010. The Nup107–160 complexand gamma-TuRC regulate microtubule polymerization at kinetochores. Nat. Cell Biol. 12:164–69
71. Capelson M, Hetzer MW. 2009. The role of nuclear pores in gene regulation, development and disease.EMBO Rep. 10:697–705
72. Zhang X, Chen S, Yoo S, Chakrabarti S, Zhang T, et al. 2008. Mutation in nuclear pore componentNUP155 leads to atrial fibrillation and early sudden cardiac death. Cell 135:1017–27
73. Kohler A, Hurt E. 2010. Gene regulation by nucleoporins and links to cancer. Mol. Cell 38:6–1574. Callan HG, Tomlin SG. 1950. Experimental studies on amphibian oocyte nuclei. I. Investigation of
the structure of the nuclear membrane by means of the electron microscope. Proc. R. Soc. Lond. Ser. B137:367–78
75. Watson ML. 1959. Further observations on the nuclear envelope of the animal cell. J. Biophys. Biochem.Cytol. 6:147–56
76. Gall JG. 1967. Octagonal nuclear pores. J. Cell Biol. 32:391–9977. Hinshaw JE, Milligan RA. 2003. Nuclear pore complexes exceeding eightfold rotational symmetry.
J. Struct. Biol. 141:259–6878. Unwin PN, Milligan RA. 1982. A large particle associated with the perimeter of the nuclear pore complex.
J. Cell Biol. 93:63–7579. Jarnik M, Aebi U. 1991. Toward a more complete 3-D structure of the nuclear pore complex. J. Struct.
Biol. 107:291–30880. Stoffler D, Feja B, Fahrenkrog B, Walz J, Typke D, Aebi U. 2003. Cryo-electron tomography provides
novel insights into nuclear pore architecture: implications for nucleocytoplasmic transport. J. Mol. Biol.328:119–30
81. Beck M, Forster F, Ecke M, Plitzko JM, Melchior F, et al. 2004. Nuclear pore complex structure anddynamics revealed by cryoelectron tomography. Science 306:1387–90
82. Franke WW, Scheer U. 1970. The ultrastructure of the nuclear envelope of amphibian oocytes: areinvestigation. I. The mature oocyte. J. Ultrastruct. Res. 30:288–316
83. Ris H. 1989. Three-dimensional imaging of cell ultrastructure with high resolution low-voltage SEM.Inst. Phys. Conf. Ser. 98:657–62
84. Goldberg MW, Allen TD. 1992. High resolution scanning electron microscopy of the nuclear envelope:demonstration of a new, regular, fibrous lattice attached to the baskets of the nucleoplasmic face of thenuclear pores. J. Cell Biol. 119:1429–40
85. Kiseleva E, Allen TD, Rutherford S, Bucci M, Wente SR, Goldberg MW. 2004. Yeast nuclear porecomplexes have a cytoplasmic ring and internal filaments. J. Struct. Biol. 145:272–88
86. Hinshaw JE, Carragher BO, Milligan RA. 1992. Architecture and design of the nuclear pore complex.Cell 69:1133–41
87. Akey CW, Radermacher M. 1993. Architecture of the Xenopus nuclear pore complex revealed by three-dimensional cryo-electron microscopy. J. Cell Biol. 122:1–19
88. Akey CW. 1995. Structural plasticity of the nuclear pore complex. J. Mol. Biol. 248:273–9389. Frenkiel-Krispin D, Maco B, Aebi U, Medalia O. 2010. Structural analysis of a metazoan nuclear pore
complex reveals a fused concentric ring architecture. J. Mol. Biol. 395:578–8690. Yang Q, Rout MP, Akey CW. 1998. Three-dimensional architecture of the isolated yeast nuclear pore
complex: functional and evolutionary implications. Mol. Cell 1:223–3491. Chadrin A, Hess B, San Roman M, Gatti X, Lombard B, et al. 2010. Pom33, a novel transmembrane
nucleoporin required for proper nuclear pore complex distribution. J. Cell Biol. 189:795–811
www.annualreviews.org • Nuclear Pore Complex Structure 639
Ann
u. R
ev. B
ioch
em. 2
011.
80:6
13-6
43. D
ownl
oade
d fr
om w
ww
.ann
ualr
evie
ws.
org
by M
arsh
all U
nive
rsity
on
11/2
8/11
. For
per
sona
l use
onl
y.
BI80CH26-Hoelz ARI 16 May 2011 12:36
92. Siniossoglou S, Wimmer C, Rieger M, Doye V, Tekotte H, et al. 1996. A novel complex of nucleoporins,which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores. Cell 84:265–75
93. Siniossoglou S, Lutzmann M, Santos-Rosa H, Leonard K, Mueller S, et al. 2000. Structure and assemblyof the Nup84p complex. J. Cell Biol. 149:41–54
94. Lutzmann M, Kunze R, Buerer A, Aebi U, Hurt E. 2002. Modular self-assembly of a Y-shaped multi-protein complex from seven nucleoporins. EMBO J. 21:387–97
95. Lutzmann M, Kunze R, Stangl K, Stelter P, Toth KF, et al. 2005. Reconstitution of Nup157 andNup145N into the Nup84 complex. J. Biol. Chem. 280:18442–51
96. Vasu S, Shah S, Orjalo A, Park M, Fischer WH, Forbes DJ. 2001. Novel vertebrate nucleoporins Nup133and Nup160 play a role in mRNA export. J. Cell Biol. 155:339–54
97. Fontoura BM, Blobel G, Matunis MJ. 1999. A conserved biogenesis pathway for nucleoporins: proteolyticprocessing of a 186-kDa precursor generates Nup98 and the novel nucleoporin, Nup96. J. Cell Biol.144:1097–112
98. Walther TC, Alves A, Pickersgill H, Loiodice I, Hetzer M, et al. 2003. The conserved Nup107–160complex is critical for nuclear pore complex assembly. Cell 113:195–206
99. Franz C, Walczak R, Yavuz S, Santarella R, Gentzel M, et al. 2007. MEL-28/ELYS is required for therecruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO Rep.8:165–72
100. Rasala BA, Orjalo AV, Shen Z, Briggs S, Forbes DJ. 2006. ELYS is a dual nucleoporin/kinetochoreprotein required for nuclear pore assembly and proper cell division. Proc. Natl. Acad. Sci. USA 103:17801–6
101. Devos D, Dokudovskaya S, Alber F, Williams R, Chait BT, et al. 2004. Components of coated vesiclesand nuclear pore complexes share a common molecular architecture. PLoS Biol. 2:2085–93
102. Aitchison JD, Blobel G, Rout MP. 1995. Nup120p: a yeast nucleoporin required for NPC distributionand mRNA transport. J. Cell Biol. 131:1659–75
103. Heath CV, Copeland CS, Amberg DC, Del Priore V, Snyder M, Cole CN. 1995. Nuclear pore complexclustering and nuclear accumulation of Poly(A)+ RNA associated with mutation of the Saccharomycescerevisiae RAT2/NUP120 gene. J. Cell Biol. 131:1677–97
104. Dockendorff TC, Heath CV, Goldstein AL, Snay CA, Cole CN. 1997. C-terminal truncations of theyeast nucleoporin Nup145p produce a rapid temperature-conditional mRNA export defect and alter-ations to nuclear structure. Mol. Cell. Biol. 17:906–20
105. Boehmer T, Enninga J, Dales S, Blobel G, Zhong H. 2003. Depletion of a single nucleoporin, Nup107,prevents the assembly of a subset of nucleoporins into the nuclear pore complex. Proc. Natl. Acad. Sci.USA 100:981–85
106. Harel A, Orjalo AV, Vincent T, Lachish-Zalait A, Vasu S, et al. 2003. Removal of a single pore subcomplexresults in vertebrate nuclei devoid of nuclear pores. Mol. Cell 11:853–64
107. Baı SW, Rouquette J, Umeda M, Faigle W, Loew D, et al. 2004. The fission yeast Nup107–120 complexfunctionally interacts with the small GTPase Ran/Spi1 and is required for mRNA export, nuclear poredistribution, and proper cell division. Mol. Cell. Biol. 24:6379–92
108. Drin G, Casella JF, Gautier R, Boehmer T, Schwartz TU, Antonny B. 2007. A general amphipathicalpha-helical motif for sensing membrane curvature. Nat. Struct. Mol. Biol. 14:138–46
109. Fath S, Mancias JD, Bi X, Goldberg J. 2007. Structure and organization of coat proteins in the COPIIcage. Cell 129:1325–36
110. Whittle JR, Schwartz TU. 2010. Structure of the Sec13-Sec16 edge element, a template for assembly ofthe COPII vesicle coat. J. Cell Biol. 190:347–61
111. Kampmann M, Blobel G. 2009. Three-dimensional structure and flexibility of a membrane-coatingmodule of the nuclear pore complex. Nat. Struct. Mol. Biol. 16:782–88
112. Debler EW, Hsia KC, Nagy V, Seo HS, Hoelz A. 2010. Characterization of a membrane-coating buildingblock: paradigm for the nuclear pore complex structure. Nucleus 1:150–57
113. Stagg SM, Gurkan C, Fowler DM, LaPointe P, Foss TR, et al. 2006. Structure of the Sec13/31 COPIIcoat cage. Nature 439:234–38
114. Stagg SM, LaPointe P, Razvi A, Gurkan C, Potter CS, et al. 2008. Structural basis for cargo regulationof COPII coat assembly. Cell 134:474–84
640 Hoelz · Debler · Blobel
Ann
u. R
ev. B
ioch
em. 2
011.
80:6
13-6
43. D
ownl
oade
d fr
om w
ww
.ann
ualr
evie
ws.
org
by M
arsh
all U
nive
rsity
on
11/2
8/11
. For
per
sona
l use
onl
y.
BI80CH26-Hoelz ARI 16 May 2011 12:36
115. Hsia KC, Hoelz A. 2010. Crystal structure of alpha-COP in complex with epsilon-COP provides insightinto the architecture of the COPI vesicular coat. Proc. Natl. Acad. Sci. USA 107:11271–76
116. Lee C, Goldberg J. 2010. Structure of coatomer cage proteins and the relationship among COPI, COPII,and clathrin vesicle coats. Cell 142:123–32
117. Fotin A, Cheng Y, Sliz P, Grigorieff N, Harrison SC, et al. 2004. Molecular model for a completeclathrin lattice from electron cryomicroscopy. Nature 432:573–79
118. Hawryluk-Gara LA, Shibuya EK, Wozniak RW. 2005. Vertebrate Nup53 interacts with the nuclearlamina and is required for the assembly of a Nup93-containing complex. Mol. Biol. Cell 16:2382–94
119. Patel SS, Rexach MF. 2008. Discovering novel interactions at the nuclear pore complex using bead halo:a rapid method for detecting molecular interactions of high and low affinity at equilibrium. Mol. Cell.Proteomics 7:121–31
120. Onischenko E, Stanton LH, Madrid AS, Kieselbach T, Weis K. 2009. Role of the Ndc1 interactionnetwork in yeast nuclear pore complex assembly and maintenance. J. Cell Biol. 185:475–91
121. Kosova B, Pante N, Rollenhagen C, Hurt E. 1999. Nup192p is a conserved nucleoporin with a preferentiallocation at the inner site of the nuclear membrane. J. Biol. Chem. 274:22646–51
122. Nehrbass U, Rout MP, Maguire S, Blobel G, Wozniak RW. 1996. The yeast nucleoporin Nup188pinteracts genetically and physically with the core structures of the nuclear pore complex. J. Cell Biol.133:1153–62
123. Grandi P, Doye V, Hurt EC. 1993. Purification of NSP1 reveals complex formation with ‘GLFG’nucleoporins and a novel nuclear pore protein NIC96. EMBO J. 12:3061–71
124. Galy V, Mattaj IW, Askjaer P. 2003. Caenorhabditis elegans nucleoporins Nup93 and Nup205 determinethe limit of nuclear pore complex size exclusion in vivo. Mol. Biol. Cell 14:5104–15
125. Grandi P, Schlaich N, Tekotte H, Hurt EC. 1995. Functional interaction of Nic96p with a core nucle-oporin complex consisting of Nsp1p, Nup49p and a novel protein Nup57p. EMBO J. 14:76–87
126. Miller BR, Powers M, Park M, Fischer W, Forbes DJ. 2000. Identification of a new vertebrate nucleo-porin, Nup188, with the use of a novel organelle trap assay. Mol. Biol. Cell 11:3381–96
127. Handa N, Kukimoto-Niino M, Akasaka R, Kishishita S, Murayama K, et al. 2006. The crystal structureof mouse Nup35 reveals atypical RNP motifs and novel homodimerization of the RRM domain. J. Mol.Biol. 363:114–24
128. Birney E, Kumar S, Krainer AR. 1993. Analysis of the RNA-recognition motif and RS and RGG domains:conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res. 21:5803–16
129. Wente SR, Rout MP, Blobel G. 1992. A new family of yeast nuclear pore complex proteins. J. Cell Biol.119:705–23
130. Belgareh N, Snay-Hodge C, Pasteau F, Dagher S, Cole CN, Doye V. 1998. Functional characterizationof a Nup159p-containing nuclear pore subcomplex. Mol. Biol. Cell 9:3475–92
131. Hurwitz ME, Strambio-de-Castillia C, Blobel G. 1998. Two yeast nuclear pore complex proteins in-volved in mRNA export form a cytoplasmically oriented subcomplex. Proc. Natl. Acad. Sci. USA 95:11241–45
132. Grandi P, Emig S, Weise C, Hucho F, Pohl T, Hurt EC. 1995. A novel nuclear pore protein Nup82pwhich specifically binds to a fraction of Nsp1p. J. Cell Biol. 130:1263–73
133. Guan T, Muller S, Klier G, Pante N, Blevitt JM, et al. 1995. Structural analysis of the p62 complex,an assembly of O-linked glycoproteins that localizes near the central gated channel of the nuclear porecomplex. Mol. Biol. Cell 6:1591–603
134. Hu T, Gerace L. 1998. cDNA cloning and analysis of the expression of nucleoporin p45. Gene 221:245–53135. Hu T, Guan T, Gerace L. 1996. Molecular and functional characterization of the p62 complex, an
assembly of nuclear pore complex glycoproteins. J. Cell Biol. 134:589–601136. Akey CW. 1990. Visualization of transport-related configurations of the nuclear pore transporter. Biophys.
J. 58:341–55137. Bayliss R, Littlewood T, Stewart M. 2000. Structural basis for the interaction between FxFG nucleoporin
repeats and importin-beta in nuclear trafficking. Cell 102:99–108138. Bayliss R, Littlewood T, Strawn LA, Wente SR, Stewart M. 2002. GLFG and FxFG nucleoporins bind
to overlapping sites on importin-beta. J. Biol. Chem. 277:50597–606
www.annualreviews.org • Nuclear Pore Complex Structure 641
Ann
u. R
ev. B
ioch
em. 2
011.
80:6
13-6
43. D
ownl
oade
d fr
om w
ww
.ann
ualr
evie
ws.
org
by M
arsh
all U
nive
rsity
on
11/2
8/11
. For
per
sona
l use
onl
y.
BI80CH26-Hoelz ARI 16 May 2011 12:36
139. Ribbeck K, Gorlich D. 2001. Kinetic analysis of translocation through nuclear pore complexes. EMBOJ. 20:1320–30
140. Liu SM, Stewart M. 2005. Structural basis for the high-affinity binding of nucleoporin Nup1p to theSaccharomyces cerevisiae importin-beta homologue, Kap95p. J. Mol. Biol. 349:515–25
141. Bednenko J, Cingolani G, Gerace L. 2003. Importin beta contains a COOH-terminal nucleoporinbinding region important for nuclear transport. J. Cell Biol. 162:391–401
142. Isgro TA, Schulten K. 2005. Binding dynamics of isolated nucleoporin repeat regions to importin-beta.Structure 13:1869–79
143. Richards SA, Carey KL, Macara IG. 1997. Requirement of guanosine triphosphate-bound Ran forsignal-mediated nuclear protein export. Science 276:1842–44
144. Nehrbass U, Blobel G. 1996. Role of the nuclear transport factor p10 in nuclear import. Science 272:120–22
145. Ribbeck K, Lipowsky G, Kent HM, Stewart M, Gorlich D. 1998. NTF2 mediates nuclear import ofRan. EMBO J. 17:6587–98
146. Smith A, Brownawell A, Macara IG. 1998. Nuclear import of Ran is mediated by the transport factorNTF2. Curr. Biol. 8:1403–6
147. Stewart M, Kent HM, McCoy AJ. 1998. Structural basis for molecular recognition between nucleartransport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran. J. Mol. Biol.277:635–46
148. Bayliss R, Leung SW, Baker RP, Quimby BB, Corbett AH, Stewart M. 2002. Structural basis for theinteraction between NTF2 and nucleoporin FxFG repeats. EMBO J. 21:2843–53
149. Fribourg S, Braun IC, Izaurralde E, Conti E. 2001. Structural basis for the recognition of a nucleoporinFG repeat by the NTF2-like domain of the TAP/p15 mRNA nuclear export factor. Mol. Cell 8:645–56
150. Grant RP, Neuhaus D, Stewart M. 2003. Structural basis for the interaction between the Tap/NXF1UBA domain and FG nucleoporins at 1 A resolution. J. Mol. Biol. 326:849–58
151. Alcazar-Roman AR, Tran EJ, Guo S, Wente SR. 2006. Inositol hexakisphosphate and Gle1 activate theDEAD-box protein Dbp5 for nuclear mRNA export. Nat. Cell Biol. 8:711–16
152. Weirich CS, Erzberger JP, Flick JS, Berger JM, Thorner J, Weis K. 2006. Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNAexport. Nat. Cell Biol. 8:668–76
153. Napetschnig J, Kassube SA, Debler EW, Wong RW, Blobel G, Hoelz A. 2009. Structural and func-tional analysis of the interaction between the nucleoporin Nup214 and the DEAD-box helicase Ddx19.Proc. Natl. Acad. Sci. USA 106:3089–94
154. von Moeller H, Basquin C, Conti E. 2009. The mRNA export protein DBP5 binds RNA and thecytoplasmic nucleoporin NUP214 in a mutually exclusive manner. Nat. Struct. Mol. Biol. 16:247–54
155. Collins R, Karlberg T, Lehtio L, Schutz P, Van Den Berg S, et al. 2009. The DEXD/H-box RNAhelicase DDX19 is regulated by an α-helical switch. J. Biol. Chem. 284:10296–300
156. Dossani ZY, Weirich CS, Erzberger JP, Berger JM, Weis K. 2009. Structure of the C-terminus of themRNA export factor Dbp5 reveals the interaction surface for the ATPase activator Gle1. Proc. Natl.Acad. Sci. USA 106:16251–56
157. Teixeira MT, Siniossoglou S, Podtelejnikov S, Benichou JC, Mann M, et al. 1997. Two functionallydistinct domains generated by in vivo cleavage of Nup145p: a novel biogenesis pathway for nucleoporins.EMBO J. 16:5086–97
158. Hodel AE, Hodel MR, Griffis ER, Hennig KA, Ratner GA, et al. 2002. The three-dimensional struc-ture of the autoproteolytic, nuclear pore-targeting domain of the human nucleoporin Nup98. Mol. Cell10:347–58
159. Rosenblum JS, Blobel G. 1999. Autoproteolysis in nucleoporin biogenesis. Proc. Natl. Acad. Sci. USA96:11370–75
160. Sun Y, Guo HC. 2008. Structural constraints on autoprocessing of the human nucleoporin Nup98.Protein Sci. 17:494–505
161. Robinson MA, Park S, Sun ZY, Silver PA, Wagner G, Hogle JM. 2005. Multiple conformations in theligand-binding site of the yeast nuclear pore-targeting domain of Nup116p. J. Biol. Chem. 280:35723–32
642 Hoelz · Debler · Blobel
Ann
u. R
ev. B
ioch
em. 2
011.
80:6
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y.
BI80CH26-Hoelz ARI 16 May 2011 12:36
162. Sampathkumar P, Ozyurt SA, Do J, Bain KT, Dickey M, et al. 2010. Structures of the autoproteolyticdomain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145. Proteins 78:1992–98
163. Yaseen NR, Blobel G. 1999. GTP hydrolysis links initiation and termination of nuclear import on thenucleoporin Nup358. J. Biol. Chem. 274:26493–502
164. Matunis MJ, Coutavas E, Blobel G. 1996. A novel ubiquitin-like modification modulates the partitioningof the Ran-GTPase-activating protein RanGAP1 between the cytosol and the nuclear pore complex.J. Cell Biol. 135:1457–70
165. Vetter IR, Nowak C, Nishimoto T, Kuhlmann J, Wittinghofer A. 1999. Structure of a Ran-bindingdomain complexed with Ran bound to a GTP analogue: implications for nuclear transport. Nature398:39–46
166. Reverter D, Lima CD. 2005. Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex. Nature 435:687–92
167. Yaseen NR, Blobel G. 1999. Two distinct classes of Ran-binding sites on the nucleoporin Nup-358.Proc. Natl. Acad. Sci. USA 96:5516–21
168. Higa MM, Alam SL, Sundquist WI, Ullman KS. 2007. Molecular characterization of the Ran-bindingzinc finger domain of Nup153. J. Biol. Chem. 282:17090–100
169. Schrader N, Koerner C, Koessmeier K, Bangert JA, Wittinghofer A, et al. 2008. The crystal structureof the Ran-Nup153ZnF2 complex: a general Ran docking site at the nuclear pore complex. Structure16:1116–25
170. Partridge JR, Schwartz TU. 2009. Crystallographic and biochemical analysis of the Ran-binding zincfinger domain. J. Mol. Biol. 391:375–89
171. Conti E, Uy M, Leighton L, Blobel G, Kuriyan J. 1998. Crystallographic analysis of the recognition ofa nuclear localization signal by the nuclear import factor karyopherin alpha. Cell 94:193–204
172. Matsuura Y, Lange A, Harreman MT, Corbett AH, Stewart M. 2003. Structural basis for Nup2p functionin cargo release and karyopherin recycling in nuclear import. EMBO J. 22:5358–69
173. Matsuura Y, Stewart M. 2005. Nup50/Npap60 function in nuclear protein import complex disassemblyand importin recycling. EMBO J. 24:3681–89
174. Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, et al. 2007. Determining the architecturesof macromolecular assemblies. Nature 450:683–94
175. Brohawn SG, Schwartz TU. 2009. A lattice model of the nuclear pore complex. Commun. Integr. Biol.2:205–7
176. Leksa NC, Schwartz TU. 2010. Membrane-coating lattice scaffolds in the nuclear pore and vesicle coats:commonalities, differences, challenges. Nucleus 1:314–18
www.annualreviews.org • Nuclear Pore Complex Structure 643
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Annual Review ofBiochemistry
Volume 80, 2011Contents
Preface
Past, Present, and Future Triumphs of BiochemistryJoAnne Stubbe � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �v
Prefatory
From Serendipity to TherapyElizabeth F. Neufeld � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 1
Journey of a Molecular BiologistMasayasu Nomura � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �16
My Life with NatureJulius Adler � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �42
Membrane Vesicle Theme
Protein Folding and Modification in the MammalianEndoplasmic ReticulumIneke Braakman and Neil J. Bulleid � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �71
Mechanisms of Membrane Curvature SensingBruno Antonny � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 101
Biogenesis and Cargo Selectivity of AutophagosomesHilla Weidberg, Elena Shvets, and Zvulun Elazar � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 125
Membrane Protein Folding and Insertion Theme
Introduction to Theme “Membrane Protein Folding and Insertion”Gunnar von Heijne � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 157
Assembly of Bacterial Inner Membrane ProteinsRoss E. Dalbey, Peng Wang, and Andreas Kuhn � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 161
β-Barrel Membrane Protein Assembly by the Bam ComplexChristine L. Hagan, Thomas J. Silhavy, and Daniel Kahne � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 189
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Transmembrane Communication: General Principles and Lessonsfrom the Structure and Function of the M2 Proton Channel, K+
Channels, and Integrin ReceptorsGevorg Grigoryan, David T. Moore, and William F. DeGrado � � � � � � � � � � � � � � � � � � � � � � � � 211
Biological Mass Spectrometry Theme
Mass Spectrometry in the Postgenomic EraBrian T. Chait � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 239
Advances in the Mass Spectrometry of Membrane Proteins:From Individual Proteins to Intact ComplexesNelson P. Barrera and Carol V. Robinson � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 247
Quantitative, High-Resolution Proteomics for Data-DrivenSystems BiologyJurgen Cox and Matthias Mann � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 273
Applications of Mass Spectrometry to Lipids and MembranesRichard Harkewicz and Edward A. Dennis � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 301
Cellular Imaging Theme
Emerging In Vivo Analyses of Cell Function UsingFluorescence ImagingJennifer Lippincott-Schwartz � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 327
Biochemistry of Mobile Zinc and Nitric Oxide Revealedby Fluorescent SensorsMichael D. Pluth, Elisa Tomat, and Stephen J. Lippard � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 333
Development of Probes for Cellular Functions Using FluorescentProteins and Fluorescence Resonance Energy TransferAtsushi Miyawaki � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 357
Reporting from the Field: Genetically Encoded Fluorescent ReportersUncover Signaling Dynamics in Living Biological SystemsSohum Mehta and Jin Zhang � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 375
Recent Advances in Biochemistry
DNA Replicases from a Bacterial PerspectiveCharles S. McHenry � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 403
Genomic and Biochemical Insights into the Specificity of ETSTranscription FactorsPeter C. Hollenhorst, Lawrence P. McIntosh, and Barbara J. Graves � � � � � � � � � � � � � � � � � � � 437
viii Contents
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Signals and Combinatorial Functions of Histone ModificationsTamaki Suganuma and Jerry L. Workman � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 473
Assembly of Bacterial RibosomesZahra Shajani, Michael T. Sykes, and James R. Williamson � � � � � � � � � � � � � � � � � � � � � � � � � � � � 501
The Mechanism of Peptidyl Transfer Catalysis by the RibosomeEdward Ki Yun Leung, Nikolai Suslov, Nicole Tuttle, Raghuvir Sengupta,
and Joseph Anthony Piccirilli � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 527
Amyloid Structure: Conformational Diversity and ConsequencesBrandon H. Toyama and Jonathan S. Weissman � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 557
AAA+ Proteases: ATP-Fueled Machines of Protein DestructionRobert T. Sauer and Tania A. Baker � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 587
The Structure of the Nuclear Pore ComplexAndre Hoelz, Erik W. Debler, and Gunter Blobel � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 613
Benchmark Reaction Rates, the Stability of Biological Moleculesin Water, and the Evolution of Catalytic Power in EnzymesRichard Wolfenden � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 645
Biological Phosphoryl-Transfer Reactions: Understanding Mechanismand CatalysisJonathan K. Lassila, Jesse G. Zalatan, and Daniel Herschlag � � � � � � � � � � � � � � � � � � � � � � � � � � � 669
Enzymatic Transition States, Transition-State Analogs, Dynamics,Thermodynamics, and LifetimesVern L. Schramm � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 703
Class I Ribonucleotide Reductases: Metallocofactor Assemblyand Repair In Vitro and In VivoJoseph A. Cotruvo Jr. and JoAnne Stubbe � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 733
The Evolution of Protein Kinase Inhibitors from Antagoniststo Agonists of Cellular SignalingArvin C. Dar and Kevan M. Shokat � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 769
Glycan Microarrays for Decoding the GlycomeCory D. Rillahan and James C. Paulson � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 797
Cross Talk Between O-GlcNAcylation and Phosphorylation:Roles in Signaling, Transcription, and Chronic DiseaseGerald W. Hart, Chad Slawson, Genaro Ramirez-Correa, and Olof Lagerlof � � � � � � � � � 825
Regulation of Phospholipid Synthesis in the YeastSaccharomyces cerevisiaeGeorge M. Carman and Gil-Soo Han � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 859
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Sterol Regulation of Metabolism, Homeostasis, and DevelopmentJoshua Wollam and Adam Antebi � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 885
Structural Biology of the Toll-Like Receptor FamilyJin Young Kang and Jie-Oh Lee � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 917
Structure-Function Relationships of the G Domain, a CanonicalSwitch MotifAlfred Wittinghofer and Ingrid R. Vetter � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 943
STIM Proteins and the Endoplasmic Reticulum-PlasmaMembrane JunctionsSilvia Carrasco and Tobias Meyer � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 973
Amino Acid Signaling in TOR ActivationJoungmok Kim and Kun-Liang Guan � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �1001
Mitochondrial tRNA Import and Its Consequencesfor Mitochondrial TranslationAndre Schneider � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �1033
Caspase Substrates and Cellular RemodelingEmily D. Crawford and James A. Wells � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �1055
Regulation of HSF1 Function in the Heat Stress Response:Implications in Aging and DiseaseJulius Anckar and Lea Sistonen � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �1089
Indexes
Cumulative Index of Contributing Authors, Volumes 76–80 � � � � � � � � � � � � � � � � � � � � � � � � � �1117
Cumulative Index of Chapter Titles, Volumes 76–80 � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �1121
Errata
An online log of corrections to Annual Review of Biochemistry articles may be found athttp://biochem.annualreviews.org/errata.shtml
x Contents
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