Protein Data Bank (PDB): The single global macromolecular structure archive

Stephen K. Burley, Helen M. Berman, Gerard J. Kleywegt, John L. Markley, Haruki Nakamura, Sameer Velankar

Research output: Chapter in Book/Report/Conference proceedingChapter

58 Citations (Scopus)

Abstract

The Protein Data Bank (PDB)––the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes––was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org), which includes 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 four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currently acts as the archive keeper, ensuring disaster recovery of PDB data and coordinating weekly updates. wwPDB partners disseminate the same archival data from multiple FTP sites, while operating complementary websites that provide their own views of PDB data with selected value-added information and links to related data resources. At present, the PDB archives experimental data, associated metadata, and 3D-atomic level structural models derived from three well-established methods: crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy (3DEM). wwPDB partners are working closely with experts in related experimental areas (small-angle scattering, chemical cross-linking/mass spectrometry, Forster energy resonance transfer or FRET, etc.) to establish a federation of data resources that will support sustainable archiving and validation of 3D structural models and experimental data derived from integrative or hybrid methods.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages627-641
Number of pages15
DOIs
StatePublished - Jan 1 2017

Publication series

NameMethods in Molecular Biology
Volume1607

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Databases
Proteins
Structural Models
Small Angle Scattering
Fluorescence Resonance Energy Transfer
Crystallography
Biological Science Disciplines
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Mass Spectrometry
Electron Microscopy
Japan
Magnetic Resonance Spectroscopy
Software

All Science Journal Classification (ASJC) codes

  • Genetics
  • Molecular Biology

Keywords

  • 3D electron microscopy
  • Chemical Component Dictionary
  • Crystallography
  • Integrative or hybrid methods
  • NEF
  • NMR Exchange Format
  • NMR spectroscopy
  • NMR-STAR
  • PDB
  • PDBx/mmCIF
  • Protein Data Bank
  • Worldwide Protein Data Bank
  • wwPDB

Cite this

Burley, S. K., Berman, H. M., Kleywegt, G. J., Markley, J. L., Nakamura, H., & Velankar, S. (2017). Protein Data Bank (PDB): The single global macromolecular structure archive. In Methods in Molecular Biology (pp. 627-641). (Methods in Molecular Biology; Vol. 1607). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7000-1_26
Burley, Stephen K. ; Berman, Helen M. ; Kleywegt, Gerard J. ; Markley, John L. ; Nakamura, Haruki ; Velankar, Sameer. / Protein Data Bank (PDB) : The single global macromolecular structure archive. Methods in Molecular Biology. Humana Press Inc., 2017. pp. 627-641 (Methods in Molecular Biology).
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Burley, SK, Berman, HM, Kleywegt, GJ, Markley, JL, Nakamura, H & Velankar, S 2017, Protein Data Bank (PDB): The single global macromolecular structure archive. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1607, Humana Press Inc., pp. 627-641. https://doi.org/10.1007/978-1-4939-7000-1_26

Protein Data Bank (PDB) : The single global macromolecular structure archive. / Burley, Stephen K.; Berman, Helen M.; Kleywegt, Gerard J.; Markley, John L.; Nakamura, Haruki; Velankar, Sameer.

Methods in Molecular Biology. Humana Press Inc., 2017. p. 627-641 (Methods in Molecular Biology; Vol. 1607).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Protein Data Bank (PDB): The single global macromolecular structure archive. In Methods in Molecular Biology. Humana Press Inc. 2017. p. 627-641. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-7000-1_26