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
dkhendrix@lbl.gov
Structural classification of RNA
http://scor.lbl.gov
Search by
• PDB or NDB id
• primary sequence
• key word
Directed Acyclic Graph
Architecture
Classification principles
Base pairing
• Watson Crick
Base stacking
• non-canonical
Sequence
Backbone conformation
•Backbone interactions
• backbone-backbone
• backbone-base
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 Holbrook
JMB 320:455 (2002)
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)
Structural, or 3-d motifs
•Distinguished from
secondary structural motifs
by three-dimensional
features and interactions
– bases: pairing, stacking,
base-backbone
– backbone: backbonebackbone, 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 1.2
Internal
Loops
NonWatson
Crick paired
stacked
duplexes
Loops with
unpaired
stacked
bases, no
triples or
dinucleotide
platforms
One
Looped
out base
One looped- Loops with
out base with Dinucleotide
stacked non- platform
Watson Crick
base pairs
Several
loopedout bases
Base triple,
no
dinucleotide
platform
Unpaired,
unstacked
looped in
bases
Transglycosidic
bond(s)
Limitations of the hierarchical classification
(SCOR 1.1, 1.2)
Internal
Loops
NonWatson
Crick paired
stacked
duplexes
Loops with
unpaired
stacked
bases, no
triples or
dinucleotide
platforms
Several
loopedout bases
One
Looped
out base
One loopedout base with
stacked nonWatson Crick
base pairs
Base triple,
no
dinucleotide
platform
Unpaired,
unstacked
looped in
bases
Transglycosidic
bond(s)
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)
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
NonWatson
Crick paired
stacked
duplexes
Loops with
unpaired
stacked
bases, no
triples or
dinucleotide
platforms
Several
loopedout bases
One
Looped
out base
One loopedout base with
stacked nonWatson Crick
base pairs
Base triple,
no
dinucleotide
platform
Unpaired,
unstacked
looped in
bases
Transglycosidic
bond(s)
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)
SCOR 2.0 DAG: internal loop base triples
Internal
Loops
Loops with
dinucleotide
platforms
Loops with simple
dinucleotide platform
Loops with
base triples
Loops with a
dinucleotide
platform
in a triple
Loops with base triples,
no 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
•PDB ID: 1dul
attributes
•Location:
chain b, res 146-150; chain b, res 161-165
•Sequence
146-UCAGG-150
165-GACGA-161
•Base pairings
146-165; U∙G; cis WC-WC
147-164; C∙A; trans WC/Hoogsteen
148-163; A∙C; trans WC/sugar edge
149-162; G∙G; trans bifurcated/Hoogsteen
150-161; G∙A; cis WC-WC
•Base stacking
Adjacent: 145-146, 146-147, 148-149, 149-150…
Non-adjacent: 147-162, 148-164 (stack swap)
•Pseudotorsions
Residue
146.B
147.B
148.B
η
169.3
160.9
110.7
θ
195.0
144.3
155.2
χ
203.9
217.6
228.2
•RNA “Rotamers”
…
•Identify motifs that consist of these more
atomic attributes.
1dul:146-150.b, 161-165.b
E. coli SRP/RNA
Batey, et al., Science 287:1232 (2000)
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
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
Often conserved
Evolutionarily conserved
Usually single
feature
Multiple features/elements
Multiple in each interacting
motif
Found within
various motifs
Not nested; may occur in
tertiary interaction motifs
May include multiple
elements and motifs
Structural
Conservation
Features
(pairing, stacking,
etc.)
Occurrence
By definition
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, coplanar residues that form a nonWatson 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)
Noncanonical
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)
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?