Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2017:1607:627-641.
doi: 10.1007/978-1-4939-7000-1_26.

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

Stephen K Burley  1   2   3 , Helen M Berman  4 , Gerard J Kleywegt  5 , John L Markley  6 , Haruki Nakamura  7 , Sameer Velankar  5
Affiliations
Review

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

Stephen K Burley et al. Methods Mol Biol. 2017.

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.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
Growth of the PDB Archive since 1971
Fig. 2
Fig. 2
wwPDB Deposition, Biocuration, and Validation Pipeline. Each box represents a modular component of the data processing workflow
Fig. 3
Fig. 3
World map showing global distribution of PDB Depositors (2012–2015)
See this image and copyright information in PMC

Similar articles

  • RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.
    Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Ghosh S, Goodsell DS, Green RK, Guranovic V, Henry J, Hudson BP, Khokhriakov I, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Webb B, Westbrook JD, Whetstone S, Young JY, Zalevsky A, Zardecki C. Burley SK, et al. Protein Sci. 2022 Dec;31(12):e4482. doi: 10.1002/pro.4482. Protein Sci. 2022. PMID: 36281733 Free PMC article.
  • The Protein Data Bank Archive.
    Velankar S, Burley SK, Kurisu G, Hoch JC, Markley JL. Velankar S, et al. Methods Mol Biol. 2021;2305:3-21. doi: 10.1007/978-1-0716-1406-8_1. Methods Mol Biol. 2021. PMID: 33950382 Review.
  • RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education.
    Burley SK, Berman HM, Christie C, Duarte JM, Feng Z, Westbrook J, Young J, Zardecki C. Burley SK, et al. Protein Sci. 2018 Jan;27(1):316-330. doi: 10.1002/pro.3331. Epub 2017 Nov 11. Protein Sci. 2018. PMID: 29067736 Free PMC article. Review.
  • Remediation of the protein data bank archive.
    Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM. Henrick K, et al. Nucleic Acids Res. 2008 Jan;36(Database issue):D426-33. doi: 10.1093/nar/gkm937. Epub 2007 Dec 11. Nucleic Acids Res. 2008. PMID: 18073189 Free PMC article.
  • The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.
    Berman H, Henrick K, Nakamura H, Markley JL. Berman H, et al. Nucleic Acids Res. 2007 Jan;35(Database issue):D301-3. doi: 10.1093/nar/gkl971. Epub 2006 Nov 16. Nucleic Acids Res. 2007. PMID: 17142228 Free PMC article.
See all similar articles

Cited by

See all "Cited by" articles

References

    1. Protein Data Bank. Protein Data Bank. Nature New Biology. 1971;233:223. - PubMed
    1. Kendrew JC, Bodo G, Dintzis HM, et al. A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature. 1958;181:662–666. - PubMed
    1. Kendrew JC, Dickerson RE, Strandberg BE, et al. Structure of myoglobin: a three-dimensional Fourier synthesis at 2 Å resolution. Nature. 1960;185:422–427. - PubMed
    1. Bolton W, Perutz MF. Three dimensional fourier synthesis of horse deoxyhaemoglobin at 2.8 Ångstrom units resolution. Nature. 1970;228:551–552. - PubMed
    1. Perutz MF, Rossmann MG, Cullis AF, et al. Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5 Å resolution, obtained by X-ray analysis. Nature. 1960;185:416–422. - PubMed

MeSH terms

LinkOut - more resources

-