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The Protein Data Bank (PDB) • PDB is the principal repository for protein structures • Established in 1971 • Accessed at http://www.rcsb.org/pdb or simply http://www.pdb.org • Currently contains over 32,000 structure entities Updated 9/05 Page 287 structures PDB content growth (www.pdb.org) year Fig. 9.6 Page 281 PDB holdings (September, 2005) 29,876 1,338 1,500 13 32,727 proteins, peptides protein/nucl. complexes nucleic acids carbohydrates total Table 9-2 Page 281 gateways to access PDB files Swiss-Prot, NCBI, EMBL Protein Data Bank CATH, Dali, SCOP, FSSP databases that interpret PDB files Fig. 9.10 Page 285 Access to PDB through NCBI You can access PDB data at the NCBI several ways. • Go to the Structure site, from the NCBI homepage • Use Entrez • Perform a BLAST search, restricting the output to the PDB database Page 289 Access to PDB through NCBI Molecular Modeling DataBase (MMDB) Cn3D (“see in 3D” or three dimensions): structure visualization software Vector Alignment Search Tool (VAST): view multiple structures Page 291 Fig. 9.15 Page 290 Fig. 9.15 Page 290 Fig. 9.16 Page 291 Fig. 9.16 Page 291 Fig. 9.16 Page 291 Fig. 9.16 Page 291 Fig. 9.16 Page 291 Fig. 9.17 Page 292 Access to structure data at NCBI: VAST Vector Alignment Search Tool (VAST) offers a variety of data on protein structures, including -- PDB identifiers -- root-mean-square deviation (RMSD) values to describe structural similarities -- NRES: the number of equivalent pairs of alpha carbon atoms superimposed -- percent identity Page 294 Many databases explore protein structures SCOP CATH Dali Domain Dictionary FSSP Page 293 Structural Classification of Proteins (SCOP) SCOP describes protein structures using a hierarchical classification scheme: Classes Folds Superfamilies (likely evolutionary relationship) Families Domains Individual PDB entries http://scop.mrc-lmb.cam.ac.uk/scop/ Page 293 Class, Architecture, Topology, and Homologous Superfamily (CATH) database CATH clusters proteins at four levels: C Class (a, b, a&b folds) A Architecture (shape of domain, e.g. jelly roll) T Topology (fold families; not necessarily homologous) H Homologous superfamily http://www.biochem.ucl.ac.uk/basm/cath_new Page 293 SCOP statistics (September, 2005) Class All a All b a/b a+b … Total # folds 218 144 136 279 945 a/b = parallel b sheets a+b = antiparallel b sheets # superfamilies 376 290 222 409 1539 # families 608 560 629 717 2845 Table 9-4 Page 298 Fig. 9.23 Page 298 Fig. 9.24 Page 299 Fig. 9.25 Page 300 Fig. 9.25 Page 300 Fig. 9.26 Page 301 Fig. 9.27 Page 302 Fig. 9.28 Page 303 Dali Domain Dictionary Dali contains a numerical taxonomy of all known structures in PDB. Dali integrates additional data for entries within a domain class, such as secondary structure predictions and solvent accessibility. Page 302 Fig. 9.29 Page 303 Fig. 9.30 Page 304 Fig. 9.30 Page 304 Fig. 9.30 Page 304 Fold classification based on structure-structure alignment of proteins (FSSP) FSSP is based on a comprehensive comparison of PDB proteins (greater than 30 amino acids in length). Representative sets exclude sequence homologs sharing > 25% amino acid identity. The output includes a “fold tree.” http://www.ebi.ac.uk/dali/fssp Page 293 Fig. 9.31 Page 305 FSSP: fold tree Fig. 9.32 Page 306 Fig. 9.33 Page 307 Fig. 9.34 Page 307 Approaches to predicting protein structures There are about >20,000 structures in PDB, and about 1 million protein sequences in SwissProt/ TrEMBL. For most proteins, structural models derive from computational biology approaches, rather than experimental methods. The most reliable method of modeling and evaluating new structures is by comparison to previously known structures. This is comparative modeling. An alternative is ab initio modeling. Page 303-305 Approaches to predicting protein structures obtain sequence (target) fold assignment comparative modeling ab initio modeling build, assess model Fig. 9.35 Page 308 Comparative modeling of protein structures [1] Perform fold assignment (e.g. BLAST, CATH, SCOP); identify structurally conserved regions [2] Align the target (unknown protein) with the template. This is performed for >30% amino acid identity over a sufficient length [3] Build a model [4] Evaluate the model Page 305 Errors in comparative modeling Errors may occur for many reasons [1] Errors in side-chain packing [2] Distortions within correctly aligned regions [3] Errors in regions of target that do not match template [4] Errors in sequence alignment [5] Use of incorrect templates Page 306 Comparative modeling In general, accuracy of structure prediction depends on the percent amino acid identity shared between target and template. For >50% identity, RMSD is often only 1 Å. Page 306 Baker and Sali (2000) Fig. 9.36 Page 308 Comparative modeling Many web servers offer comparative modeling services. Examples are SWISS-MODEL (ExPASy) Predict Protein server (Columbia) WHAT IF (CMBI, Netherlands) Page 309