Organization of RNA structural motifs:

Lessons from SCORDonna K. HendrixDepartment of Plant and Microbial BiologyUniversity of California, Berkeley andPhysical Biosciences DivisionLawrence Berkeley National Laboratorydkhendrix@lbl.gov

Structural classification of RNAhttp://scor.lbl.gov

Search by • PDB or NDB id• primary sequence• key word

Directed Acyclic Graph Architecture

Classification principles

•Backbone interactions• backbone-backbone

• backbone-base

Base stackingBase pairing• Watson Crick• non-canonical

SequenceBackbone conformation

SCOR 2.0 classification Structural classification

• Hairpin loops • Internal loops

Tertiary interactions• Ribose zippers • Coaxial helices, Tetraloop-receptor, A-minor motif, Kissing hairpin, Pseudoknots

Functional classification• Molecular function• Motif function• Structural models

RNA structural classification• Conserved patterns and relationships

• sequence• structure

• Organize data for non-specialist• Classification for RNA model-building, engineering

How to give yourself eye strain

SCOR 2.0.3 update:

• 102 new structures

• 20 structures removed from SCOR 2.0.2

• 85 structures previously in SCOR but not functionally annotated

Moved server from LBL; cleaned up the code a little bit; upgraded OS/tomcat; Eric added apache services.

What defines an RNA structural motif?

Conserved, repeated structural features– sequence– fold (backbone, stacking)– interactions (hydrogen bonds, stacking)

Primary structure

•Identify by– conservation of

sequence– binding or stability

•Specify by sequence:– GUAUGA (Box C of

C/D Box snoRNA)– CUCAGUACGAGAGG

AAC (sarcin-ricin loop)

M. Tamura and S.R HolbrookJMB 320:455 (2002)

Secondary structure motifs

1euy, Sherlin, et. Al. JMB 299:431 (2000)

•Specify by Watson Crick base pairing– internal loops– hairpin loops– junction loops– some tertiary interactions (pseudoknots)

Structural, or 3-d motifs

•Distinguished from secondary structural motifs by three-dimensional features and interactions

– bases: pairing, stacking, base-backbone

– backbone: backbone-backbone, torsion angles (including chi), pseudotorsion

•Described by sequence, secondary structure features as well

1euy, Sherlin, et. Al. JMB 299:431 (2000)

Organization of structural motifs: hierarchical classification from SCOR 1.1

and 1.2Internal Loops

Loops with Dinucleotide platform

Base triple, no dinucleotide platform

Trans- glycosidic bond(s)

One Looped out base

Non-Watson Crick paired stacked duplexes

Unpaired, unstacked looped in bases

Loops with unpaired stacked bases, no triples or dinucleotide platforms

One looped-out base with stacked non-Watson Crick base pairs

Several looped-out bases

Limitations of the hierarchical classification (SCOR 1.1, 1.2)

Internal Loops

Base triple, no dinucleotide platform

Trans- glycosidic bond(s)

One Looped out base

Non-Watson Crick paired stacked duplexes

Unpaired, unstacked looped in bases

Loops with unpaired stacked bases, no triples or dinucleotide platforms

Several looped-out bases

Loops with Dinucleotide platform

One looped-out base with stacked non-Watson Crick base pairs

1exy:a:9,20,22 (G,C,A)Jiang, et al. Structure 7:1461 (1999)

1i6u: c:10-11, c:28 (A-U)ATishchenko, et al., JMB 311:311 (2001)

Organization of structural motifs:SCOR 2.0 and the DAG classification

• Use a directed acyclic graph (DAG) to represent the relationships among motifs

• Increase searching options: by sequence, strand, PDB or NDB identifier, residue number and key words

Limitations of the hierarchical

classification(SCOR 1.1, 1.2) Internal Loops

Base triple, no dinucleotide platform

Trans- glycosidic bond(s)

One Looped out base

Non-Watson Crick paired stacked duplexes

Unpaired, unstacked looped in bases

Loops with unpaired stacked bases, no triples or dinucleotide platforms

Several looped-out bases

Loops with Dinucleotide platform

One looped-out base with stacked non-Watson Crick base pairs

1exy:a:9,20,22 (G,C,A)Jiang, et al. Structure 7:1461 (1999)

1i6u: c:10-11, c:28 (A-U)ATishchenko, et al., JMB 311:311 (2001)

SCOR 2.0 DAG: internal loop base triples

Internal Loops

Loops with dinucleotide platforms

Loops with base triples

Loops with adinucleotide platformin a triple

Loops with base triples,no dinucleotide platformLoops with simple

dinucleotide platform

Limitations of the DAG

•No clean way to present orthogonal attributes– “hairball”– Multiple DAGs

•Not easily searchable– Inherent awkwardness to browsing

Organization of structural motifs:hierarchically organized queryable

attributes

1dul:146-150.b, 161-165.bE. coli SRP/RNABatey, et al., Science 287:1232 (2000)

•PDB ID: 1dul•Location:

chain b, res 146-150; chain b, res 161-165•Sequence

146-UCAGG-150165-GACGA-161

•Base pairings146-165; U∙G; cis WC-WC147-164; C∙A; trans WC/Hoogsteen148-163; A∙C; trans WC/sugar edge149-162; G∙G; trans bifurcated/Hoogsteen150-161; G∙A; cis WC-WC

•Base stackingAdjacent: 145-146, 146-147, 148-149, 149-150…Non-adjacent: 147-162, 148-164 (stack swap)

•PseudotorsionsResidue η θ χ146.B 169.3 195.0 203.9147.B 160.9 144.3 217.6148.B 110.7 155.2 228.2

•RNA “Rotamers”…

•Identify motifs that consist of these more atomic attributes.

Feature-based structural classification

• *Sequence• *Loop length• Base pairings• Pseudotorsion angles • Hydrogen bonds • Stacking

– adjacent and non-adjacent

Classification of structural elements by features

Feature-based searching and characterization of motifs

Characteristic Element Loop Motifs Tertiary Interaction Motifs

Size Small, local May span entire loop Multiple loops, stems involved

Sequence Conservation

Little or none Often have sequence preferences/isosteric

Interaction sites

Structural Conservation

By definition Often conserved Evolutionarily conserved

Features(pairing, stacking,

etc.)

Usually single feature

Multiple features/elements Multiple in each interacting motif

Occurrence Found within various motifs

Not nested; may occur in tertiary interaction motifs

May include multiple elements and motifs

RNA Structural Elements

Element Name(s)

Description Found In Reference

U turn/Uridine turn/Pi turn

A sharp bend in the phosphate-sugar backbone between the first and second nucleotides, followed by characteristic stacking of the second and third nucleotides. Original descriptions include a stabilizing hydrogen bond between the first and third residues.

Hairpin loops (e.g., GNRA, T--C loop) and internal loops

(Holbrook et al., 1978; Kim and Sussman, 1976; Klosterman et al., 2004b; Quigley and Rich, 1976)

A-minor interaction

The insertion of minor groove edges of an adenine into the minor groove of neighboring helices. Four types have been identified.

Ribose zipper, kink-turn (Nissen et al., 2001)

S-turn Two consecutive bends in the phosphate-sugar backbone characterized by backbone distortions and inverted sugar puckers, resulting in an "S" shape.

Loop E motifSarcin-ricin loop

(Correll et al., 1999; Szewczak et al., 1993; Wimberly et al., 1993)

Dinucleotide platform

Two adjacent, covalently linked, co-planar residues that form a non-Watson Crick pairing.

Internal loops, often involved in a base triple

(Klosterman et al., 2004b)

Base triples Three hydrogen-bonded, coplanar bases with two of the bases sometimes forming a Watson-Crick pair or dinucleotide platform.

Loop E motif, Sarcin-ricin loop

(Klosterman et al., 2004b)

Cross-strand stack

A base on one strand stacks with a base on the opposing strand, rather than stacking with the adjacent bases on its own strand.

Internal loops, e.g., Bacterial Loop E motif

(Correll et al., 1997)

Non-canonical base pairs

Two bases of any type interacting in a generally planar arrangement can form hydrogen bonds in characteristic patterns.

Double helices (Leontis and Westhof, 2001) (Nagaswamy et al., 2002)

Extruded helical single strand

Two or three unpaired bases extruded from the main double helical stack forming an independent stack.

Internal and hairpin loops (Klosterman et al., 2004b)

Backbone rotamers

Commonly occurring RNA backbone conformations.

Double helices, hairpin, internal and junction loops

(Duarte et al., 2003; Hershkovitz et al., 2003; Murray et al., 2003; Schneider et al., 2004)

Annotation issues: What is a motif?

Recurrent structure

Conserved structure

Conserved function?

I know it when I see it.

Definition (glossary)

Annotation issues: Assessment

Canonical

Variations (-like, pseudo-, reverse-, inverse-)

eVal

Annotation issues: Who is it for?

Student.

Naïve in knowledge of structural motifs, but expert in biology.

Expert.

Computer-readable, human-interpretable?

But what about my favorite structure (sequence, motif)?

BLAST?