Protein Data Bank

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Protein Data Bank
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Data formatmmCIF, PDB
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The Protein Data Bank (PDB)[1] is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, NMR spectroscopy, and, increasingly, cryogenic electron microscopy. All submitted data are reviewed by expert biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication.[2] Global access to the data is provided by the websites of the wwPDB member organizations (PDBe,[3] PDBj,[4] RCSB PDB,[5] BMRB[6] and the EMDB[7]).

The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene Ontology.[8][9]

History

Two forces converged to initiate the PDB: a small but growing collection of sets of protein structure data determined by X-ray diffraction; and the newly available (1968) molecular graphics display, the Brookhaven RAster Display (BRAD), to visualize these protein structures in 3-D. In 1969, with the sponsorship of Walter Hamilton at the Brookhaven National Laboratory, Edgar Meyer (Texas A&M University) began to write software to store atomic coordinate files in a common format to make them available for geometric and graphical evaluation. By 1971, one of Meyer's programs, SEARCH, enabled researchers to remotely access information from the database to study protein structures offline.[10] SEARCH was instrumental in enabling networking, thus marking the functional beginning of the PDB.

The Protein Data Bank was announced in October 1971 in Nature New Biology[11] as a joint venture between Cambridge Crystallographic Data Centre, UK and Brookhaven National Laboratory, US.

Upon Hamilton's death in 1973, Tom Koetzle took over direction of the PDB for the subsequent 20 years. In January 1994, Joel Sussman of Israel's Weizmann Institute of Science was appointed head of the PDB. In October 1998,[12] the PDB was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB);[13] the transfer was completed in June 1999. The new director was Helen M. Berman of Rutgers University (one of the managing institutions of the RCSB, the other being the San Diego Supercomputer Center at UC San Diego).[14] In 2003, with the formation of the wwPDB, the PDB became an international organization. The founding members are PDBe (Europe),[3] RCSB (US), and PDBj (Japan).[4] The Biological Magnetic Resonance Data Bank (BMRB)[6] joined in 2006. The Electron Microscopy Data Bank (EMDB)[15] joined in 2021. Each of the five members of wwPDB can act as deposition, data processing and distribution centers for PDB data. The data processing refers to the fact that wwPDB staff review and annotate each submitted entry.[16] The data are then automatically checked for plausibility (the source code[17] for this validation software has been made available to the public at no charge).

Contents

The PDB database is updated weekly (UTC+0 Wednesday), along with its holdings list.[18] As of 21 May 2026, the PDB comprises the following:

Molecular type X-ray diffraction Electron microscopy NMR Integrative Multiple methods Neutron Total
Proteins only 181,265 23,360 12,819 350 231 84 218,109
Proteins with oligosaccharides 10,500 3,754 34 8 11 1 14,308
Protein/Nucleic Acid
complexes 		9,212 6,856 287 26 8 0 16,389
Nucleic Acids only 3,161 27 1,580 3 15 3 4,789
Other 178 27 35 4 0 0 244
Oligosaccharides only 11 0 6 0 1 0 18
Total: 204,327 34,316 14,761 391 266 88 254,149
194,485 structures in the PDB have a structure factor file.
11,505 structures have an NMR restraint file.
6,038 structures in the PDB have a chemical shifts file.
33,747 structures in the PDB have a 3DEM map file deposited in EM Data Bank
Rate of protein structure determination techniques over the decades. MX = macromolecular crystallography, 3DEM = 3D Electron microscopy.[19]

Most structures are determined by X-ray diffraction, but about 7% of structures are determined by protein NMR. When using X-ray diffraction, approximations of the coordinates of the atoms of the protein are obtained, whereas using NMR, the distance between pairs of atoms of the protein is estimated. The final conformation of the protein is obtained from NMR by solving a distance geometry problem. After 2013, a growing number of proteins are determined by cryo-electron microscopy.

For PDB structures determined by X-ray diffraction that have a structure factor file, their electron density map may be viewed. The data of such structures may be viewed on the three PDB websites.

Historically, the number of structures in the PDB has grown at an approximately exponential rate, with 100 registered structures in 1982, 1,000 structures in 1993, 10,000 in 1999, 100,000 in 2014, and 200,000 in January 2023.[20][21]

PDB-IHM

PDB-Dev was a database also managed by wwPDB, for structural models arising from a "integrative" or "hybrid" approach, i.e. combining experiment and structure prediction. Included models use the same four-character accession code format. In 2024, PDB-Dev was renamed to PDB-IHM and unified into the PDB: its structures can now be accessed from regular wwPDB endpoints including websites. As of January 2026, PDB-IHM contains 382 entries.[22]

File format

Script error: No such module "Labelled list hatnote". The file format initially used by the PDB was called the PDB file format. The original format was restricted by the width of computer punch cards to 80 characters per line. Around 1996, the "macromolecular Crystallographic Information file" format, mmCIF, which is an extension of the CIF format was phased in. mmCIF became the standard format for the PDB archive in 2014.[23] In 2019, the wwPDB announced that depositions for crystallographic methods would only be accepted in mmCIF format.[24]

An XML version of PDB, called PDBML, was described in 2005.[25] The structure files can be downloaded in any of these three formats, though an increasing number of structures do not fit the legacy PDB format. Individual files are easily downloaded into graphics packages from Internet URLs:

  • For PDB format files, use, e.g., http://www.pdb.org/pdb/files/4hhb.pdb.gz or http://pdbe.org/download/4hhb
  • For PDBML (XML) files, use, e.g., http://www.pdb.org/pdb/files/4hhb.xml.gz or http://pdbe.org/pdbml/4hhb

The "4hhb" is the PDB identifier. Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. (This is not a unique identifier for biomolecules, because several structures for the same molecule—in different environments or conformations—may be contained in PDB with different PDB IDs.)

Viewing the data

The structure files may be viewed using one of several free and open source computer programs, including Jmol, Pymol, VMD, Molstar and Rasmol. Other non-free, shareware programs include ICM-Browser,[26] MDL Chime, UCSF Chimera, Swiss-PDB Viewer,[27] StarBiochem[28] (a Java-based interactive molecular viewer with integrated search of protein databank), Sirius, and VisProt3DS[29] (a tool for Protein Visualization in 3D stereoscopic view in anaglyph and other modes), and Discovery Studio. The RCSB PDB website contains an extensive list of both free and commercial molecule visualization programs and web browser plugins.

See also

References

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  1. ^ Page Module:Citation/CS1/styles.css has no content.wwPDB, Consortium (2019). "Protein Data Bank: the single global archive for 3D macromolecular structure data". Nucleic Acids Res. 47 (D1): 520–528. doi:10.1093/nar/gky949. PMC 6324056. PMID 30357364.
  2. ^ Page Module:Citation/CS1/styles.css has no content.wwPDB.org. "wwPDB: Usage Policies". www.wwpdb.org. Retrieved 2024-04-16.
  3. ^ a b Page Module:Citation/CS1/styles.css has no content."PDBe home < Node < EMBL-EBI". pdbe.org.
  4. ^ a b Page Module:Citation/CS1/styles.css has no content."Protein Data Bank Japan – PDB Japan – PDBj". pdbj.org.
  5. ^ Page Module:Citation/CS1/styles.css has no content.Bank, RCSB Protein Data. "RCSB PDB: Homepage". rcsb.org.
  6. ^ a b Page Module:Citation/CS1/styles.css has no content."Biological Magnetic Resonance Bank". bmrb.wisc.edu. Archived from the original on 2020-10-20. Retrieved 2006-09-13.
  7. ^ Page Module:Citation/CS1/styles.css has no content.EMDB, EMBL-EBI. "EMDB: Homepage". www.emdatabank.org.
  8. ^ Page Module:Citation/CS1/styles.css has no content.Berman, H. M. (January 2008). "The Protein Data Bank: a historical perspective" (PDF). Acta Crystallographica Section A. A64 (1): 88–95. doi:10.1107/S0108767307035623. PMID 18156675.
  9. ^ Page Module:Citation/CS1/styles.css has no content.Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM (December 1997). "PDBsum: a Web-based database of summaries and analyses of all PDB structures". Trends Biochem. Sci. 22 (12): 488–90. doi:10.1016/S0968-0004(97)01140-7. PMID 9433130.
  10. ^ Page Module:Citation/CS1/styles.css has no content.Meyer EF (1997). "The first years of the Protein Data Bank". Protein Science. 6 (7). Cambridge University Press: 1591–1597. doi:10.1002/pro.5560060724. PMC 2143743. PMID 9232661.
  11. ^ Page Module:Citation/CS1/styles.css has no content."Protein Data Bank". Nature New Biology. 233. 1971. doi:10.1038/newbio233223b0.
  12. ^ Page Module:Citation/CS1/styles.css has no content.Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (January 2000). "The Protein Data Bank". Nucleic Acids Res. 28 (1): 235–242. doi:10.1093/nar/28.1.235. PMC 102472. PMID 10592235.
  13. ^ Page Module:Citation/CS1/styles.css has no content."Research Collaboratory for Structural Bioinformatics". RCSB.org. Research Collaboratory for Structural Bioinformatics. Archived from the original on 2007-02-05.
  14. ^ Page Module:Citation/CS1/styles.css has no content."RCSB PDB Newsletter Archive". RCSB Protein Data Bank.
  15. ^ Page Module:Citation/CS1/styles.css has no content.EMDB, EMBL-EBI. "EMDB: Homepage". www.emdatabank.org.
  16. ^ Page Module:Citation/CS1/styles.css has no content.Curry E, Freitas A, O'Riáin S (2010). "The Role of Community-Driven Data Curation for Enterprises". In D. Wood (ed.). Linking Enterprise Data. Boston: Springer US. pp. 25–47. ISBN 978-1-441-97664-2.
  17. ^ Page Module:Citation/CS1/styles.css has no content."PDB Validation Suite". sw-tools.pdb.org. Archived from the original on 2016-03-03. Retrieved 2009-09-12.
  18. ^ Page Module:Citation/CS1/styles.css has no content.Bank, RCSB Protein Data. "PDB Statistics: PDB Data Distribution by Experimental Method and Molecular Type". www.rcsb.org. Retrieved 2025-11-04.
  19. ^ Page Module:Citation/CS1/styles.css has no content.Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L, Costanzo LD, et al. (wwPDB consortium) (January 2019). "Protein Data Bank: the single global archive for 3D macromolecular structure data". Nucleic Acids Research. 47 (D1): D520–D528. doi:10.1093/nar/gky949. PMC 6324056. PMID 30357364.
  20. ^ Page Module:Citation/CS1/styles.css has no content.Anon (2014). "Hard data: It has been no small feat for the Protein Data Bank to stay relevant for 100,000 structures". Nature. 509 (7500): 260. doi:10.1038/509260a. PMID 24834514.
  21. ^ Page Module:Citation/CS1/styles.css has no content.Protein Data Bank. "PDB Statistics: Overall Growth of Released Structures Per Year". www.rcsb.org. Retrieved 12 January 2023.
  22. ^ Page Module:Citation/CS1/styles.css has no content."PDB-IHM". pdb-ihm.org.
  23. ^ Page Module:Citation/CS1/styles.css has no content."wwPDB: File Formats and the PDB". wwpdb.org. Retrieved April 1, 2020.
  24. ^ Page Module:Citation/CS1/styles.css has no content.wwPDB.org. "wwPDB: 2019 News". wwpdb.org.
  25. ^ Page Module:Citation/CS1/styles.css has no content.Westbrook J, Ito N, Nakamura H, Henrick K, Berman HM (April 2005). "PDBML: the representation of archival macromolecular structure data in XML". Bioinformatics. 21 (7): 988–992. doi:10.1093/bioinformatics/bti082. PMID 15509603.
  26. ^ Page Module:Citation/CS1/styles.css has no content."ICM-Browser". Molsoft L.L.C. Retrieved 2013-04-06.
  27. ^ Page Module:Citation/CS1/styles.css has no content."Swiss PDB Viewer". Swiss Institute of Bioinformatics. Retrieved 2013-04-06.
  28. ^ Page Module:Citation/CS1/styles.css has no content."STAR: Biochem - Home". web.mit.edu.
  29. ^ Page Module:Citation/CS1/styles.css has no content."VisProt3DS". Molecular Systems Ltd. Archived from the original on 2013-07-19. Retrieved 2013-04-06.

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