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Biological 3D Structural Databases

  • Yasser GaberEmail author
  • Boshra Rashad
  • Eman Fathy
Chapter

Abstract

Structural biology is a branch of biological sciences that deals with the molecular structure of biological macromolecule structures like proteins, DNA, and RNA. Getting acquainted with spatial positions of the molecular atoms, the cavities, channels, pores, and clefts found in the macromolecular structure can explain many phenomena such as the mechanisms of protein-protein interaction, inhibition or activation of cellular receptors, antibiotic resistance, and other cellular mysteries. Designing new drugs is mostly facilitated via 3D information of the target receptor. The 3D structures can be elucidated using four major techniques, X-ray, NMR spectroscopy, cryo-electron microscopy (cryo-EM), and neutron diffraction, given that each of these techniques has its merits and demerits. Maintaining these invaluable and exponentially growing structural data is a crucial step. Therefore, data repositories known as structural databases are created where a plethora of structures are deposited and refined yearly. This chapter presents these databases and highlights their characteristic features in addition to related servers that help in storing, analysis, comparison, and classification of the 3D structural information such as RCSB PDB, PDBj, PDBe, BMRB, SCOP2, CATH, PDBsum, sc-PDB, and PDBTM.

Keywords

3D structure databases PDB PDBsum ScPDB PDB-TM SCOP CATH SC-PDB X-Ray crystallography 

References

  1. Acharya C, Kufareva I, Ilatovskiy AV, Abagyan R (2014) PeptiSite: a structural database of peptide binding sites in 4D. Biochem Biophys Res Commun 445(4):717–723PubMedPubMedCentralGoogle Scholar
  2. An J, Totrov M, Abagyan R (2005) Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteomics 4(6):752–761PubMedGoogle Scholar
  3. Andreeva A, Howorth D, Chandonia J-M, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (2007) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36(suppl_1):D419–D425PubMedPubMedCentralGoogle Scholar
  4. Babajan B, Chaitanya M, Rajsekhar C, Gowsia D, Madhusudhana P, Naveen M et al (2011) Comprehensive structural and functional characterization of Mycobacterium tuberculosis UDP-NAG enolpyruvyl transferase (Mtb-MurA) and prediction of its accurate binding affinities with inhibitors. Interdiscip Sci 3(3):204–216.  https://doi.org/10.1007/s12539-011-0100-yCrossRefPubMedGoogle Scholar
  5. Bagchi A (2012) A brief overview of a few popular and important protein databases. Computat Mol Biosci 2(04):115Google Scholar
  6. Berman HM, Bhat TN, Bourne PE, Feng Z, Gilliland G, Weissig H, Westbrook J (2000) The Protein Data Bank and the challenge of structural genomics. Nat Struct Mol Biol 7:957–959Google Scholar
  7. Berman HM, Kleywegt GJ, Nakamura H, Markley JL (2012) The Protein Data Bank at 40: reflecting on the past to prepare for the future. Structure 20(3):391–396PubMedPubMedCentralGoogle Scholar
  8. Carpenter EP, Beis K, Cameron AD, Iwata S (2008) Overcoming the challenges of membrane protein crystallography. Curr Opin Struct Biol 18(5):581–586PubMedPubMedCentralGoogle Scholar
  9. Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM (2013) The nucleic acid database: new features and capabilities. Nucleic Acids Res 42(D1):D114–D122PubMedPubMedCentralGoogle Scholar
  10. Craveur P, Rebehmed J, de Brevern AG (2014) PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins. Database:2014Google Scholar
  11. Dawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P et al (2016) CATH: an expanded resource to predict protein function through structure and sequence. Nucleic Acids Res 45(D1):D289–D295PubMedPubMedCentralGoogle Scholar
  12. Dawson NL, Sillitoe I, Lees JG, Lam SD, Orengo CA (2017) CATH-Gene3d: generation of the resource and its use in obtaining structural and functional annotations for protein sequences. Protein Bioinforma 1558:79–110Google Scholar
  13. DeLano WL (2002) The PyMOL molecular graphics system. http://pymol.org
  14. Desaphy J, Bret G, Rognan D, Kellenberger E (2014) sc-PDB: a 3D-database of ligandable binding sites—10 years on. Nucleic Acids Res 43(D1):D399–D404PubMedPubMedCentralGoogle Scholar
  15. Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66(4):486–501PubMedPubMedCentralGoogle Scholar
  16. Gaber Y (2016) In-silico smart library design to engineer a xylosetolerant hexokinase variant. Afr J Biotechnol 15(21):910–916Google Scholar
  17. Gaber Y, Mekasha S, Vaaje-Kolstad G, Eijsink VG, Fraaije MW (2016) Characterization of a chitinase from the cellulolytic actinomycete Thermobifida fusca. Biochim Biophys Acta 1864(9):1253–1259PubMedGoogle Scholar
  18. Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibrián-Uhalte E (2016) The ChEMBL database in 2017. Nucleic Acids Res 45(D1):D945–D954PubMedPubMedCentralGoogle Scholar
  19. Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C (2015) ChEBI in 2016: improved services and an expanding collection of metabolites. Nucleic Acids Res 44(D1):D1214–D1219PubMedPubMedCentralGoogle Scholar
  20. Holm L, Rosenström P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38(suppl_2):W545–W549PubMedPubMedCentralGoogle Scholar
  21. Hubbard TJ, Murzin AG, Brenner SE, Chothia C (1997) SCOP: a structural classification of proteins database. Nucleic Acids Res 25(1):236–239PubMedPubMedCentralGoogle Scholar
  22. Jo S, Im W (2012) Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Res 41(D1):D470–D474PubMedPubMedCentralGoogle Scholar
  23. Joosten RP, Te Beek TA, Krieger E, Hekkelman ML, Hooft RW, Schneider R et al (2010) A series of PDB related databases for everyday needs. Nucleic Acids Res 39(suppl_1):D411–D419PubMedPubMedCentralGoogle Scholar
  24. Kellenberger E, Muller P, Schalon C, Bret G, Foata N, Rognan D (2006) sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank. J Chem Inf Model 46(2):717–727PubMedGoogle Scholar
  25. Kinjo AR, Bekker G-J, Suzuki H, Tsuchiya Y, Kawabata T, Ikegawa Y, Nakamura H (2016) Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Res 45:D282–D288.  https://doi.org/10.1093/nar/gkw962CrossRefPubMedPubMedCentralGoogle Scholar
  26. Knudsen M, Wiuf C (2010) The CATH database. Hum Genomics 4(3):207PubMedPubMedCentralGoogle Scholar
  27. Kozma D, Simon I, Tusnady GE (2012) PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Res 41(D1):D524–D529PubMedPubMedCentralGoogle Scholar
  28. Krieger E, Vriend G (2014) YASARA View—molecular graphics for all devices—from smartphones to workstations. Bioinformatics 30(20):2981–2982PubMedPubMedCentralGoogle Scholar
  29. Laskowski RA (2007) Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature. Bioinformatics 23(14):1824–1827PubMedGoogle Scholar
  30. Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM (2018) PDBsum: structural summaries of PDB entries. Protein Sci 27(1):129–134PubMedGoogle Scholar
  31. Ledford H (2010) Big science: the cancer genome challenge. Nat News 464(7291):972–974Google Scholar
  32. Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C (2000) SCOP: a structural classification of proteins database. Nucleic Acids Res 28(1):257–259PubMedPubMedCentralGoogle Scholar
  33. Lobanov MY, Shoemaker BA, Garbuzynskiy SO, Fong JH, Panchenko AR, Galzitskaya OV (2009) ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. Nucleic Acids Res 38(suppl_1):D283–D287PubMedPubMedCentralGoogle Scholar
  34. Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH (2013) MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res 42(D1):D297–D303PubMedPubMedCentralGoogle Scholar
  35. Markley JL, Ulrich EL, Berman HM, Henrick K, Nakamura H, Akutsu H (2008) BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR 40(3):153–155PubMedPubMedCentralGoogle Scholar
  36. Mewes H-W, Frishman D, Güldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Münsterkötter M, Rudd S, Weil B (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res 30(1):31–34PubMedPubMedCentralGoogle Scholar
  37. Pavelka A, Chovancova E, Damborsky J (2009) HotSpot Wizard: a web server for identification of hot spots in protein engineering. Nucleic Acids Res 37(suppl_2):W376–W383PubMedPubMedCentralGoogle Scholar
  38. Perutz MF, Rossmann MG, Cullis AF, Muirhead H, Will G, North A (1960) Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-Å resolution obtained by X-ray analysis. Nature 185(4711):416PubMedGoogle Scholar
  39. Popenda M, Szachniuk M, Blazewicz M, Wasik S, Burke EK, Blazewicz J, Adamiak RW (2010) RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinformatics 11(1):231PubMedPubMedCentralGoogle Scholar
  40. Putignano V, Rosato A, Banci L, Andreini C (2017) MetalPDB in 2018: a database of metal sites in biological macromolecular structures. Nucleic Acids Res 46(D1):D459–D464PubMedCentralGoogle Scholar
  41. Rosenbaum DM, Rasmussen SG, Kobilka BK (2009) The structure and function of G-protein-coupled receptors. Nature 459(7245):356PubMedPubMedCentralGoogle Scholar
  42. Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11(9):739–747PubMedGoogle Scholar
  43. Shindyalov IN, Bourne PE (2001) A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. Nucleic Acids Res 29(1):228–229PubMedPubMedCentralGoogle Scholar
  44. Stansfeld PJ, Goose JE, Caffrey M, Carpenter EP, Parker JL, Newstead S, Sansom MS (2015) MemProtMD: automated insertion of membrane protein structures into explicit lipid membranes. Structure 23(7):1350–1361PubMedPubMedCentralGoogle Scholar
  45. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J et al (2007) BioMagResBank. Nucleic Acids Res 36(suppl_1):D402–D408PubMedPubMedCentralGoogle Scholar
  46. Varadi M, Tompa P (2015) The protein ensemble database. Intrinsically disordered proteins studied by NMR spectroscopy. Springer, pp 335–349Google Scholar
  47. Velankar S, Alhroub Y, Alili A, Best C, Boutselakis HC, Caboche S et al (2010) PDBe: protein data bank in Europe. Nucleic Acids Res 39(suppl_1):D402–D410PubMedPubMedCentralGoogle Scholar
  48. Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P (2015) PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res 44(D1):D385–D395PubMedPubMedCentralGoogle Scholar
  49. Wang XT, Chan TF, Lam V, Engel PC (2008) What is the role of the second “structural” NADP+-binding site in human glucose 6-phosphate dehydrogenase? Protein Sci 17(8):1403–1411PubMedPubMedCentralGoogle Scholar
  50. Wlodawer A, Minor W, Dauter Z, Jaskolski M (2008) Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J 275(1):1–21PubMedGoogle Scholar
  51. Yeats C, Maibaum M, Marsden R, Dibley M, Lee D, Addou S, Orengo CA (2006) Gene3D: modelling protein structure, function and evolution. Nucleic Acids Res 34(suppl_1):D281–D284PubMedGoogle Scholar
  52. Yin H, Flynn AD (2016) Drugging membrane protein interactions. Annu Rev Biomed Eng 18:51PubMedPubMedCentralGoogle Scholar
  53. Zanegina O, Kirsanov D, Baulin E, Karyagina A, Alexeevski A, Spirin S (2015) An updated version of NPIDB includes new classifications of DNA–protein complexes and their families. Nucleic Acids Res 44(D1):D144–D153PubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Pharmaceutics and Pharmaceutical Technology, Faculty of PharmacyMutah UniversityAl-KarakJordan
  2. 2.Microbiology Department, Faculty of PharmacyBeni-Suef UniversityBeni-SuefEgypt
  3. 3.Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS)Beni-Suef UniversityBeni-SuefEgypt
  4. 4.Microbiology DepartmentDirectorate of Health Affairs at Ministry of HealthBeni-SuefEgypt

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