1. A. niger 2aaa:1-353 Acid  -amylase B. cereus J. Biochem 113:646-649 Oligo-1,6 glucosidase B. circulans 1cdg:1-3821cgt:1-382 Cyclodextrin glycosyltransferase  -Glucanase  -Amylase (N)  -Amylase  -Galactosidase (3) B. stearothermophilus 1cyg:1-378 TIMTrp biosynthesisGlycosyltransferaseRuBisCo (C) Rossmann foldFlavodoxin-like  -Barrel  scopRoot Class Fold Superfamily Family Protein Species PDB/Ref S COP Sample ppHierarchy Determined by structure Related by homology

2. Structural classification of RNA http://scor.berkeley.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

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

4. Organization of structural motifs: hierarchically organized queryable attributes 1dul:146-150.b, 161-165.b E. coli SRP/RNA Batey, et al., Science 287:1232 (2000) 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; 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 ηθχ 146.B169.3195.0203.9 147.B160.9144.3217.6 148.B110.7155.2228.2 RNA “Rotamers” … Identify motifs that consist of these more atomic attributes.

5. SCOR 3.0: Attribute-based structural classification *Sequence *Loop length Base pairings (RNAVIEW 1 ) Backbone torsion angles (e.g., AMIGOS 2 ) Hydrogen bonds (HBExplore 3 ) Stacking –adjacent and non-adjacent Classification of structural elements by features Feature-based searching and characterization of motifs 1 H. 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. 2 C.M. Duarte and A.M. Pyle. (1998) Stepping through RNA structure: a novel approach to conformational analysis. J.Mol. Biol. 284:1465-1478. 3 K. Lindauer, C. Bendic, J. Sühnel. (1996) HBexplore - A New Tool for Identifying and Analyzing Hydrogen Bonding Patterns in Biological Macromolecules. Comput. Appl. Biosci. 12:281-289.

6. 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

7. Sarcin-Ricin Loop by Elements PDB ID 483D C.C. Correll, I.G. Wool, and A. Munishkin J. Mol. Biol 292:275 (1999)

8. Sarcin-Ricin Loop by Elements S-turn

9. Sarcin-Ricin Loop by Elements S-turn Base triple

10. Sarcin-Ricin Loop by Elements S-turnBase triple Cross-strand stack

11. Sarcin-Ricin Loop by Elements S-turn Base triple Cross-strand stack U-turn (in a tetraloop)

12. Sarcin-Ricin Loop by Elements S-turn Base triple Cross-strand stack U-turn (in a tetraloop) PLUS: Base pairings, backbone-base hydrogen bonds…