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The Protein Data Bank Archive

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Structural Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2305))

Abstract

Protein Data Bank is the single worldwide archive of experimentally determined macromolecular structure data. Established in 1971 as the first open access data resource in biology, the PDB archive is managed by the worldwide Protein Data Bank (wwPDB) consortium which has four partners—the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu). The PDB archive currently includes ~175,000 entries. The wwPDB has established a number of task forces and working groups that bring together experts form the community who provide recommendations on improving data standards and data validation for improving data quality and integrity. The wwPDB members continue to develop the joint deposition, biocuration, and validation system (OneDep) to improve data quality and accommodate new data from emerging techniques such as 3DEM. Each PDB entry contains coordinate model and associated metadata for all experimentally determined atomic structures, experimental data for the traditional structure determination techniques (X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy), validation reports, and additional information on quaternary structures. The wwPDB partners are committed to following the FAIR (Findability, Accessibility, Interoperability, and Reproducibility) principles and have implemented a DOI resolution mechanism that provides access to all the relevant files for a given PDB entry. On average, >250 new entries are added to the archive every week and made available by each wwPDB partner via FTP area. The wwPDB partner sites also develop data access and analysis tools and make these available via their websites. wwPDB continues to work with experts in the community to establish a federation of archives for archiving structures determined using integrative/hybrid method where multiple experimental techniques are used.

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Acknowledgments

The Protein Data Bank in Europe is supported by European Molecular Biology Laboratory-European Bioinformatics Institute; Wellcome Trust [104948]; Biotechnology and Biological Sciences Research Council [BB/G022577/1, BB/J007471/1, BB/K016970/1, BB/K020013/1, BB/M013146/1, BB/M011674/1, BB/M020347/1, BB/M020428/1, BB/P024351/1]; European Union [284209], ELIXIR, and Open Targets. The RCSB PDB is jointly funded by the National Science Foundation (DBI-1832184), the National Institutes of Health (R01GM133198), and the United States Department of Energy (DE-SSC0019749). PDBj is funded by the National Bioscience Database Center of Japan Science and Technology Agency (JST-NBDC), the Basis for Supporting Innovative Drug Discovery and Life Science Research of Japan Agency for Medical Research and Development (AMED-BINDS), and the Joint Usage / Research Center project assigned to Institute for Protein Research, Osaka University, by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. BMRB is supported by US National Institutes of Health (NIH) grant R01GM109046. We gratefully acknowledge contributions from John Berrisford, Aleks Gutmanas, Eldon L. Ulrich, Jasmine Young, and John Westbrook, and all wwPDB staff members present and past. We would like to acknowledge wwPDB collaborators and partners at the EMDB, SASBDB, CCP4, CCPEM, CCPN, and the global structural biology and bioinformatics communities.

Author information

Authors and Affiliations

  1. Protein Data Bank in Europe, European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK

    Sameer Velankar

  2. Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA

    Stephen K. Burley

  3. Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA

    Stephen K. Burley

  4. Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA

    Stephen K. Burley

  5. Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA

    Stephen K. Burley

  6. Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka, Japan

    Genji Kurisu

  7. BioMagResBank, Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA

    Jeffrey C. Hoch

  8. BioMagResBank, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA

    John L. Markley

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  1. Sameer Velankar
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  2. Stephen K. Burley
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  3. Genji Kurisu
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  4. Jeffrey C. Hoch
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  5. John L. Markley
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Corresponding author

Correspondence to Sameer Velankar .

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Editors and Affiliations

  1. The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK

    Raymond J. Owens

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Velankar, S., Burley, S.K., Kurisu, G., Hoch, J.C., Markley, J.L. (2021). The Protein Data Bank Archive. In: Owens, R.J. (eds) Structural Proteomics. Methods in Molecular Biology, vol 2305. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1406-8_1

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  • DOI: https://doi.org/10.1007/978-1-0716-1406-8_1

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