“the resolution revolution” - pdbj2018/11/11 · cell, 2016 flexibility in biomolecule 23...
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“The Resolution Revolution”Werner Kühlbrandt, Science, 2014
“Liberty Leading the People”
painted by Eugène Delacroix
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構造データベースから見えてくる電子顕微鏡による構造解析の動向
鈴木 博文早稲田大学先進理工学部
CrSJ2018 ランチョンセミナー2018-11-11 東工大
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Two viewpoints 3
Cryo-EM (3DEM) data in databanks
1. Comparison to crystallography
Methodology outline
[raw data] [map] [atomic model]
2. Comparison to NMR
Ensemble structure of molecule in solution
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Background:
Cryo-EM data in databanks
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Yearly statistics of EMDB & PDB deposition 5
Number: EMDB & PDB entries
EM Navigator statistics
https://pdbj.org/emnavi/
Year
Resolution
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Direct electron detector 6
motion correction
Resolution, sensitivity, & speed improved
scintillator
CCD array
fiber optics
e- e- e- e-e-
CMOS
e- e- e- e-e-
Micrographs as movie
Legacy CCD camera Direct electron detector
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High resolution detectors 7D
ete
cto
r
Resolution
Number: EMDB & PDB entries
EM Navigator statistics
https://pdbj.org/emnavi/
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wwPDB collaboration 8
DepositionArchive
distribution
Search Visualization
PDB, EMDB,& BMRB
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EM Navigator et al. 9
EM Navigator
https://pdbj.org/emnavi/
Yorodumi
Omokage search
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PDBx version 5 10
News in wwPDB website
www.wwpdb.org
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Comparison
to crystallography
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Similarity in methods 12
Crystallography 3DEM
Rawdata
Aligned? Yes No
Phase? No Yes
↓ Initial model/phase required
Initial mapcan help
Densitymap
↓Initial model required for low-res. data
Atomicmodel Refine
Refine
Refine
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EM data in Yorodumi (万見) 13
PHENIX v2411 is used for refinement
Restraint parameters during refinementScreenshot of Yorodumi
data: PDB-5ool
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Difference in methods 14
Crystallography 3DEM
Rawdata
Aligned? Yes No
Phase? No Yes
↓ Initial model/phase required
Initial mapcan help
Densitymap
↓Initial model required for low-res. data
Atomicmodel Refine
Refine
Refine
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Map + model view of EM data 15
Map-model fitting
as movieEMDB-8819
PDB-5wek
Yorodumi-Molmil
Ligand binding site
focus view
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New PDB data in Yorodumi 16
PDB-5vot
Buffer solution details
Software details
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Databanks for each 17
Crystallography
3DEM
(incl. electron
crystallography)
Raw
data- EMPIAR
Density
mapPDB
(structure factor)EMDB
Atomic
modelPDB
EM Navigator
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Databank for EM raw images 18
EMPIAR webpage by EMBL-EBI
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Comparison
to NMR
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PDB deposition NMR vs. 3DEM 20
0
200
400
600
20
09
20
10
20
11
20
12
20
13
20
14
20
15
20
16
Nikkei biotech
cryo-EM issue
Feb, 2017
NMR
EM
PDB yearly deposition
NMR vs. EM
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Structure ensembles by NMR 21
Experiment
1 sample condition
100 conformers
Deposition
20 conformers
1 entry
PDB-6ali
putative thioredoxin
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Structure ensembles by cryo-EM 22
5 samples
x (1 all + 4 classes)
= 25 PDB entries
Ryanodine receptor
(calcium channel)
des Georges et al.,
Cell, 2016
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Flexibility in biomolecule 23
flexibility, heterogeneity & inoccupancyin molecular assembly
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Classification 24
Global & unclassified
average
Class averages
Classification
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Local averaging & classification 25
Local (masked)
average
Local (masked)
classification
Classification
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Respiratory “megacomplex” 26
EMDB 6776 6776 6773 6772 6771 6774
PDB 5xti 5xth 5xtd 5xtc 5xtb 5xte
res.
(Å)17.4 3.9 3.7 3.7 3.4 3.4
IIII
IV
IIII
IV
I II
IV
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Yorodumi Papers (万見文献) 27
Search result
Details of
data entries
Database of citation of structure data
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Omokage search 28
Atomic model
ABCD
Sequence,2nd. structure,
etc.
Any
similar
data?
Comparison
& search
PDB
Typical ones (e.g. Structure Navigator of PDBj)
SAS dummy
atom model
3DEM map
Atomic model
(shape only)Any
similar
data?
SAS
BDB
EMDB
PDB
Comparison
& search
Omokage search
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Enjoy cryo-EM data
with PDBj services!
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EM Navigator https://pdbj.org/emnavi/
Yorodumi https://pdbj.org/yorodumi/
Omokage search https://pdbj.org/omokage/