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BYU BIO 465 - The Protein Data Bank (PDB)

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Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Slide 32Slide 33Slide 34Slide 35Slide 36Slide 37Slide 38Slide 39Slide 40Slide 41Slide 42Slide 43The Protein Data Bank (PDB)Page 287• 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 entitiesUpdated 9/05PDB content growth (www.pdb.org)yearstructuresFig. 9.6Page 281PDB holdings (September, 2005)29,876 proteins, peptides1,338 protein/nucl. complexes1,500 nucleic acids13 carbohydrates32,727 totalTable 9-2Page 281Protein Data Bank Swiss-Prot, NCBI, EMBL CATH, Dali, SCOP, FSSPFig. 9.10 Page 285 gateways to access PDB files databases that interpret PDB filesAccess to PDB through NCBIPage 289 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 databaseAccess to PDB through NCBIPage 291Molecular Modeling DataBase (MMDB)Cn3D (“see in 3D” or three dimensions):structure visualization software Vector Alignment Search Tool (VAST):view multiple structuresFig. 9.15 Page 290Fig. 9.15 Page 290Fig. 9.16 Page 291Fig. 9.16 Page 291Fig. 9.16 Page 291Fig. 9.16 Page 291Fig. 9.16 Page 291Fig. 9.17 Page 292Access to structure data at NCBI: VASTPage 294Vector Alignment Search Tool (VAST) offers a varietyof 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 identityMany databases explore protein structuresPage 293SCOPCATHDali Domain DictionaryFSSPStructural Classification of Proteins (SCOP)Page 293SCOP describes protein structures using a hierarchical classification scheme:ClassesFoldsSuperfamilies (likely evolutionary relationship)FamiliesDomainsIndividual PDB entrieshttp://scop.mrc-lmb.cam.ac.uk/scop/Class, Architecture, Topology, andHomologous Superfamily (CATH) databasePage 293CATH clusters proteins at four levels:C Class (, , & folds)A Architecture (shape of domain, e.g. jelly roll)T Topology (fold families; not necessarily homologous)H Homologous superfamilyhttp://www.biochem.ucl.ac.uk/basm/cath_newSCOP statistics (September, 2005)Class # folds # superfamilies # familiesAll  218 376 608All  144 290 560/ 136 222 629+ 279 409 717…Total 945 1539 2845Table 9-4Page 298 = parallel  sheets= antiparallel  sheetsFig. 9.23Page 298Fig. 9.24Page 299Fig. 9.25Page 300Fig. 9.25Page 300Fig. 9.26Page 301Fig. 9.27Page 302Fig. 9.28Page 303Dali Domain DictionaryPage 302Dali contains a numerical taxonomy of all knownstructures in PDB. Dali integrates additional data for entries within a domain class, such as secondary structure predictions and solvent accessibility.Fig. 9.29Page 303Fig. 9.30Page 304Fig. 9.30Page 304Fig. 9.30Page 304Fold classification based on structure-structurealignment of proteins (FSSP)Page 293FSSP is based on a comprehensive comparison ofPDB proteins (greater than 30 amino acids in length).Representative sets exclude sequence homologssharing > 25% amino acid identity.The output includes a “fold tree.”http://www.ebi.ac.uk/dali/fsspFig. 9.31Page 305FSSP: fold treeFig. 9.32Page 306Fig. 9.33Page 307Fig. 9.34Page 307Page 303-305There are about >20,000 structures in PDB, andabout 1 million protein sequences in SwissProt/TrEMBL. For most proteins, structural modelsderive from computational biology approaches,rather than experimental methods.The most reliable method of modeling and evaluatingnew structures is by comparison to previouslyknown structures. This is comparative modeling.An alternative is ab initio modeling. Approaches to predicting protein structuresobtain sequence (target)fold assignmentcomparativemodelingab initiomodelingbuild, assess modelFig. 9.35Page 308Approaches to predicting protein structuresPage 305[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 modelComparative modeling of protein structuresPage 306Errors 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 templatesErrors in comparative modelingPage 306In general, accuracy of structure prediction dependson the percent amino acid identity shared betweentarget and template.For >50% identity, RMSD is often only 1 Å.Comparative modelingBaker and Sali (2000)Fig. 9.36Page 308Page 309Many web servers offer comparative modeling services.Examples areSWISS-MODEL (ExPASy)Predict Protein server (Columbia)WHAT IF (CMBI, Netherlands)Comparative


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BYU BIO 465 - The Protein Data Bank (PDB)

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