1. Organization of RNA structural motifs: Lessons from SCOR
Donna K. Hendrix
Department of Plant and Microbial Biology
University of California, Berkeley
and
Physical Biosciences Division
Lawrence Berkeley National Laboratory

2. Structural classification of RNA http://scor.lbl.gov
Search by
PDB or NDB id
primary sequence
key word
Directed Acyclic Graph Architecture
SCOR 1.2 location, and what it looks like. SCOR lives today.

3. Classification principles
Base pairing
Watson Crick
non-canonical
Base stacking
Backbone conformation
Sequence
Backbone interactions
backbone-backbone
backbone-base

4. SCOR 2.0 classification Tertiary interactions Ribose zippers
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
Add location
Functional classification

5. RNA structural classification
Conserved patterns and relationships
sequence
structure
Organize data for non-specialist
Classification for RNA model-building, engineering

6. How to give yourself eye strain
SCOR 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.

7. What defines an RNA structural motif?
Conserved, repeated structural features
sequence
fold (backbone, stacking)
interactions (hydrogen bonds, stacking)

8. Primary structure Identify by Specify by sequence:
conservation of sequence
binding or stability
Specify by sequence:
GUAUGA (Box C of C/D Box snoRNA)
CUCAGUACGAGAGGAAC (sarcin-ricin loop)
M. Tamura and S.R Holbrook
JMB 320:455 (2002)

9. Secondary structure motifs
Specify by Watson Crick base pairing
internal loops
hairpin loops
junction loops
some tertiary interactions (pseudoknots)
1euy, Sherlin, et. Al. JMB 299:431 (2000)

10. 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)

11. Organization of structural motifs: hierarchical classification from SCOR 1.1 and 1.2
Internal Loops
Non-Watson Crick paired stacked duplexes
Several looped-out bases
One Looped out base
Base triple, no dinucleotide platform
Unpaired, unstacked looped in bases
Trans- glycosidic bond(s)
Loops with unpaired stacked bases, no triples or dinucleotide platforms
One looped-out base with stacked non-Watson Crick base pairs
Loops with Dinucleotide platform

12. Limitations of the hierarchical classification (SCOR 1.1, 1.2)
Internal Loops
Non-Watson Crick paired stacked duplexes
Several looped-out bases
One Looped out base
Base triple, no dinucleotide platform
Unpaired, unstacked looped in bases
Trans- glycosidic bond(s)
Loops with unpaired stacked bases, no triples or dinucleotide platforms
One looped-out base with stacked non-Watson Crick base pairs
Loops with Dinucleotide platform
1i6u: c:10-11, c:28 (A-U)A
Tishchenko, et al., JMB 311:311 (2001)
1exy:a:9,20,22 (G,C,A)
Jiang, et al. Structure 7:1461 (1999)

13. 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

14. Limitations of the hierarchical classification(SCOR 1.1, 1.2)
Internal Loops
Non-Watson Crick paired stacked duplexes
Several looped-out bases
One Looped out base
Base triple, no dinucleotide platform
Unpaired, unstacked looped in bases
Trans- glycosidic bond(s)
Loops with unpaired stacked bases, no triples or dinucleotide platforms
One looped-out base with stacked non-Watson Crick base pairs
Loops with Dinucleotide platform
1i6u: c:10-11, c:28 (A-U)A
Tishchenko, et al., JMB 311:311 (2001)
1exy:a:9,20,22 (G,C,A)
Jiang, et al. Structure 7:1461 (1999)

15. SCOR 2.0 DAG: internal loop base triples
Internal Loops
Loops with dinucleotide platforms
Loops with base triples
Loops with base triples,
no dinucleotide platform
Loops with simple
dinucleotide platform
Loops with a
dinucleotide
platform
in a triple

16. Limitations of the DAG No clean way to present orthogonal attributes
“hairball”
Multiple DAGs
Not easily searchable
Inherent awkwardness to browsing
Inherent akwardness to browsing

17. Organization of structural motifs: hierarchically organized queryable attributes
PDB ID: 1dul
Location:
chain b, res ; chain b, res
Sequence
146-UCAGG-150
165-GACGA-161
Base pairings
; U∙G; cis WC-WC
; C∙A; trans WC/Hoogsteen
; A∙C; trans WC/sugar edge
; G∙G; trans bifurcated/Hoogsteen
; G∙A; cis WC-WC
Base stacking
Adjacent: , , , …
Non-adjacent: , (stack swap)
Pseudotorsions
Residue η θ χ
146.B
147.B
148.B
RNA “Rotamers” …
Identify motifs that consist of these more atomic attributes.
Organization of queryable attributes will, itself, be structured
1dul: b, b
E. coli SRP/RNA
Batey, et al., Science 287:1232 (2000)

18. 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

19. RNA Structural Elements
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

21. 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 motif
Sarcin-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
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
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)

22. Annotation issues: What is a motif?
Recurrent structure
Conserved structure
Conserved function?
I know it when I see it.
Definition (glossary)

23. Annotation issues: Assessment
Canonical
Variations (-like, pseudo-, reverse-, inverse-)
eVal

24. 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?