Bioinforma)cs Resources - PDB -

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1 Bioinforma)cs Resources - PDB - Lecture & Exercises Prof. B. Rost, Dr. L. Richter, J. Reeb Ins)tut für Informa)k I12

2 Orga - Exam Date Exam takes place on Friday, July 31 st Room: MW 0250 (Mechanical Engineering Building) Time scheduled: (might be later) Dura)on: approx. 90 min

3 Adver)sement Bachelor thesis: Carry your Genes (CyG) In collabora)on with Certgate GmbH and Iteratec GmbH Affects: Personalized medicine, mobile apps, encryp)on Hiwi opportunity included see h\ps://

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5 PDB History 1968: Brookhaven RAster Display (BRAD) 1969: Edgar Meyer came up with a file format for atomic coordinates 1971: remote access with SEARCH program wri\en by Meyer - > PDB func)onal 1998: transfer to RCSB (Research Collaboratory for Structural Biology) 2003: forma)on of wwpdb (PDBe, RCSB, PDBj, BMRB(2006))

6 References F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E.F. Meyer Jr., M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, M. Tasumi (1977) The Protein Data Bank: a computer- based archival file for macromolecular structures. J. Mol. Biol. 112: H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank Nucleic Acids Research, 28: H.M. Berman, K. Henrick, H. Nakamura (2003) Announcing the worldwide Protein Data Bank Nature Structural Biology 10 (12): 98. h\p://

7 Current Composi)on* Experimental Method X-ray diffraction Proteins Nucleic Acids Protein/Nucleic Acid complexes Other Total Hybrid Other Total NMR Electron microscopy *May, 18th, 2015

8 Growth of PDB All Entries Yearly Total

9 Entries According to Method Total X-Ray NMR EM

10 Growth of X- Ray Structures Yearly Total

11 Growth of NMR Structures Yearly Total

12 Growth of EM Structures Yearly Total

13 Unique CATH Folds (Topologies) Yearly Total

14 Unique CATH Superfamilies Yearly Total

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16 Atomic Coordinate Entry Format aka PDB format current version 3.30 comprises 190 pages mp://mp.wwpdb.org/pub/pdb/doc/ format_descrip)ons/format_v33_a4.pdf

17 Record Format allowed characters: abcdefghijklmnopqrstuvwxyzabcdefghi JKLMNOPQRSTUVWXYZ :<>?,:; are delimiters, otherwise need to be escaped by \ a file consists of mul)ple lines each line is 80 characters wide including EOL lines are self- iden)fying: first six columns contains the record name followed by a blank

18 Single Line Records, One Time/One Line CRYST1: Unit cell parameters, space group, and Z. END: Last record in the file. HEADER: First line of the entry, contains PDB ID code, classifica)on, and date of deposi)on. NUMMDL: Number of models....

19 One Time/Mul)ple Line (incompl.) AUTHOR: List of contributors. KEYWDS: List of keywords describing the macromolecule. SOURCE: Biological source of macromolecules in the entry. TITLE: Descrip)on of the experiment represented in the entry. subsequent lines have a con)nua)on number

20 Mul)ple Times/One Line (incompl.) ATOM: Atomic coordinate records for standard groups. CONECT: Connec)vity records. DBREF: Reference to the entry in the sequence database(s). HELIX: Iden)fica)on of helical substructures. SHEET: Iden)fica)on of sheet substructures.

21 Mul)ple Times/Mul)ple Lines (incompl.) FORMUL: Chemical formula of non- standard groups. HETNAM: Compound name of the heterogens. SEQRES: Primary sequence of backbone residues. SITE: Iden)fica)on of groups comprising important en)ty sites. subsequent lines have a con)nua)on number

22 Record Order Records have to appear in a defined order There are mandatory and op)onal records Some mandatory records depends on condi)ons Mandatory records without content are NULL examples for mandatory records: - HEADER - TITLE - COMPND -...

23 Records Belongs to Sec)ons Section Record Type Title HEADER, OBSLTE, TITLE, SPLIT, CAVEAT, COMPND, SOURCE, KEYWDS,EXPDTA, NUMMDL, MDLTYP, AUTHOR, REVDAT, SPRSDE, JRNL Remark REMARKs Primary structure DBREF, SEQADV, SEQRES MODRES Secondary structure HELIX, SHEET Coordinate MODEL, ATOM, ANISOU, TER, HETATM, ENDMDL......

24 Records Even Have Formats A Records consists of fields with specified data Data could be: A- Z, a- z, atom name, a nine character string represen)ng a date, a number,... Complex data: token (string followed by : ), a comma separated list of strings, a fixed format string literal...

25 Example Header COLUMNS DATA TYPE FIELD DEFINITION Record name HEADER String(40) classification Classifies the molecule(s). * Date depdate Deposition date. This is the date the coordinates were received at the PDB IDcode idcode This identifier is unique within the PDB. * taken from a class list from the current wwpdb Annotation Documentation Appendices (

26 Classifica)on of Structures: CATH/SCOP came up in the middle of the 1990s both are quite similar aim: organize the protein structures available in PDB, based on single domains hierarchical system (roughly): - secondary structure content - fold - super families - families

27 SCOP: a Structural Classifica)on of Proteins Murzin, A., Brenner, S. E., Hubbard, T. J. P. and Chothia, C. (1995) J. Mol. Biol., 247, Hubbard, T. P., Murzin, A., Brenner, S. E. and Chothia, C. (1997), Nucl. Acids Res. 25(1), (easier to obtain) fully manually curated, driven by expert analysis associated with the ASTRAL compendium latest news: SCOPe (UC Berkeley), SCOP2 (MRC Lab Mol Biol, Cambridge, UK)

28 CATH - Faces taken from taken from

29 CATH semi- automa)c procedure for deriving a novel hierarchical classifica)on of protein domain structures four main levels: - C: protein class, mainly secondary structure composi)on of each domain - A: architecture, summarizes shapes based on orienta)on of secondary structure elements - T: topology, sequen)al connec)vity is considered - H: homologous superfamily, high similarity with similar func)ons, evolu)onary rela)onship assumed