SCOP Sample ppHierarchy

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SCOP Sample ppHierarchy
scop
Root
a
b
a/b
ab
Class
Determined by structure
Rossmann fold
Flavodoxin-like
a/b-Barrel
Fold
TIM
Trp biosynthesis
Glycosyltransferase
RuBisCo (C)
Superfamily
b-Glucanase
a-Amylase (N)
b-Amylase
b-Galactosidase (3)
Family
Acid a-amylase
Oligo-1,6 glucosidase
Cyclodextrin glycosyltransferase
Protein
Related by homology
A. niger
B. cereus
B. circulans
B. stearothermophilus
Species
2aaa1-353
J. Biochem 113646-649
1cdg1-382
1cgt1-382
1cyg1-378
PDB/Ref
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Structural classification of RNAhttp//scor.berke
ley.edu

• 579 PDB entries classified
• Structural, Functional and Tertiary Interactions
• Search by
• PDB or NDB id
• primary sequence
• key word
• Directed Acyclic Graph Architecture
• Glossary

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Classification principles

• Base pairing
• Watson Crick
• non-canonical

Base stacking
Backbone conformation
Sequence

• Backbone interactions
• backbone-backbone
• backbone-base

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Organization of structural motifshierarchically
organized queryable attributes

• PDB ID 1dul
• Location
• chain b, res 146-150 chain b, res 161-165
• Sequence
• 146-UCAGG-150
• 165-GACGA-161
• Base pairings
• 146-165 UG cis WC-WC
• 147-164 CA trans WC/Hoogsteen
• 148-163 AC trans WC/sugar edge
• 149-162 GG trans bifurcated/Hoogsteen
• 150-161 GA 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 169.3 195.0 203.9
• 147.B 160.9 144.3 217.6

1dul146-150.b, 161-165.b E. coli SRP/RNA Batey,
et al., Science 2871232 (2000)
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SCOR 3.0 Attribute-based structural
classification

• Sequence
• Loop length
• Base pairings (RNAVIEW1)
• Backbone torsion angles (e.g., AMIGOS2)
• Hydrogen bonds (HBExplore3)
• Stacking
• adjacent and non-adjacent
• Classification of structural elements by features
• Feature-based searching and characterization of
  motifs
• 1H. Yang, F. Jossinet, N. Leontis, L. Chen, J.
  Westbrook, H.M. Berman, E. Westhof. (2003) Tools
  for the automatic identification and
  classification of RNA base pairs. Nucleic Acids
  Research 31 3450-3460.
• 2C.M. Duarte and A.M. Pyle. (1998) Stepping
  through RNA structure a novel approach to
  conformational analysis. J.Mol. Biol.
  2841465-1478.
• 3K. Lindauer, C. Bendic, J. Sühnel. (1996)
  HBexplore - A New Tool for Identifying and
  Analyzing Hydrogen Bonding Patterns in Biological
  Macromolecules. Comput. Appl. Biosci. 12281-289.
  

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Characteristics of RNA Elements Vs. Motifs

• Elements/Attributes
• Local
• Single feature
• Found in different motifs
• Little sequence specificity

• Loop Motifs (Hairpin Internal)
• May span entire loop
• Multiple features
• May include elements
• Not nested in other loop motifs
• Often have sequence preferences

• Tertiary Interaction Motifs
• Multiple loop or stem interactions
• Evolutionarily conserved
• May include elements or motifs
• Often have sequence preferences

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Sarcin-Ricin Loop by Elements
PDB ID 483D C.C. Correll, I.G. Wool, and A.
Munishkin J. Mol. Biol 292275 (1999)
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Sarcin-Ricin Loop by Elements
S-turn
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Sarcin-Ricin Loop by Elements
S-turn
Base triple
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Sarcin-Ricin Loop by Elements
S-turn
Base triple
Cross-strand stack
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Sarcin-Ricin Loop by Elements
U-turn (in a tetraloop)
S-turn
Cross-strand stack
Base triple
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Sarcin-Ricin Loop by Elements
U-turn (in a tetraloop)
S-turn
Cross-strand stack
Base triple
PLUS Base pairings, backbone-base hydrogen bonds
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