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Methods Mol Biol. 2017;1607:627-641. doi: 10.1007/978-1-4939-7000-1_26.

Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

Author information

1
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics, Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA. stephen.burley@rcsb.org.
2
Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ, 08903, USA. stephen.burley@rcsb.org.
3
Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, 92093, USA. stephen.burley@rcsb.org.
4
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics, Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
5
Protein Data Bank in Europe, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
6
BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
7
Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.

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.

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

PMID:
28573592
PMCID:
PMC5823500
DOI:
10.1007/978-1-4939-7000-1_26
[Indexed for MEDLINE]
Free PMC Article

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