Protein Data Bank

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Protein Data Bank
Wwpdb-logo.png
Content
Description
Contact
Primary citation PMID 30357364
Access
Data format mmCIF, PDB
Website
  • www.wwpdb.org
  • www.pdbe.org
  • www.rcsb.org/pdb
  • www.bmrb.wisc.edu
  • www.pdbj.org

The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe,[1] PDBj,[2] RCSB,[3] and BMRB[4]). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.

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.[5][6]

History

Two forces converged to initiate the PDB: 1) a small but growing collection of sets of protein structure data determined by X-ray diffraction; and 2) 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.[7] 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[8] as a joint venture between Cambridge Crystallographic Data Centre, UK and Brookhaven National Laboratory, US.

Upon Hamilton's death in 1973, Tom Koeztle 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,[9] the PDB was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB);[10] 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).[11] In 2003, with the formation of the wwPDB, the PDB became an international organization. The founding members are PDBe (Europe),[1] RCSB (USA), and PDBj (Japan).[2] The BMRB[4] joined in 2006. Each of the four 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.[12] The data are then automatically checked for plausibility (the source code[13] for this validation software has been made available to the public at no charge).

Contents

Examples of protein structures from the PDB (created with UCSF Chimera)
Rate of Protein Structure Determination by Method and Year.[14]

The PDB database is updated weekly (UTC+0 Wednesday). Likewise, the PDB holdings list[15] is also updated weekly. As of 4 July 2019, the breakdown of current holdings is as follows:

Experimental
Method
Proteins Nucleic Acids Protein/Nucleic Acid
complexes
Other Total
X-ray diffraction 128397 2029 6628 4 137058
NMR 11112 1290 260 8 12670
Electron microscopy 2524 32 885 0 3441
Hybrid 141 5 3 1 150
Other 259 4 6 13 282
Total: 142433 3360 7782 26 153601
126,949 structures in the PDB have a structure factor file.
10,022 structures have an NMR restraint file.
3,774 structures in the PDB have a chemical shifts file.
3,484 structures in the PDB have a 3DEM map file deposited in EM Data Bank

These data show that most structures are determined by X-ray diffraction, but about 10% of structures are now determined by protein NMR. When using X-ray diffraction, approximations of the coordinates of the atoms of the protein are obtained, whereas estimations of the distances between pairs of atoms of the protein are found through NMR experiments. Therefore, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy. (Clicking on the numbers in the original table will bring up examples of structures determined by that method.)

The significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed. The data of such structures is stored on the "electron density server".[16][17]

In the past, the number of structures in the PDB has grown at an approximately exponential rate, passing the 100 registered structures milestone in 1982, the 1,000 in 1993, the 10,000 in 1999, and the 100,000 in 2014.[18][19] However, since 2007, the rate of accumulation of new protein structures appears to have plateaued.

File format

The file format initially used by the PDB was called the PDB file format. This 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 started to be phased in. mmCIF is now the master format for the PDB archive.[20] In 2019, the wwPDB announced that depositions for crystallographic methods would only be accepted in mmCIF format.[21]

An XML version of this format, called PDBML, was described in 2005.[22] 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. In fact, individual files are easily downloaded into graphics packages using web addresses:

  • 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 cannot be used as an identifier for biomolecules, because often several structures for the same molecule—in different environments or conformations—are 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, and Rasmol. Other non-free, shareware programs include ICM-Browser,[23] MDL Chime, UCSF Chimera, Swiss-PDB Viewer,[24] StarBiochem[25] (a Java-based interactive molecular viewer with integrated search of protein databank), Sirius, and VisProt3DS[26] (a tool for Protein Visualization in 3D stereoscopic view in anaglyth 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

  1. ^ a b EMBL-EBI. "PDBe home . www.pdbe.org.
  2. ^ a b "Protein Data Bank Japan - PDB Japan - PDBj". www.pdbj.org.
  3. ^ Bank, RCSB Protein Data. "RCSB PDB: Homepage". www.rcsb.org.
  4. ^ a b "BMRB - Biological Magnetic Resonance Bank". www.bmrb.wisc.edu.
  5. ^ 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.
  6. ^ 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.
  7. ^ Meyer EF (1997). "The first years of the Protein Data Bank". Protein Science. Cambridge University Press. 6 (7): 1591–1597. doi:10.1002/pro.5560060724. PMC 2143743. PMID 9232661.
  8. ^ "Protein Data Bank". Nature New Biology. 1971. doi:10.1038/newbio233223b0.
  9. ^ 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.
  10. ^ RCSB | Research Collaboratory for Structural Bioinformatics Archived 2007-02-05 at the Wayback Machine
  11. ^ "RCSB PDB Newsletter Archive". RCSB Protein Data Bank.
  12. ^ 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, MA: Springer US. pp. 25–47. ISBN 978-1-441-97664-2.
  13. ^ "PDB Validation Suite". sw-tools.pdb.org.
  14. ^ 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.
  15. ^ "PDB Current Holdings Breakdown". RCSB.
  16. ^ "The Uppsala Electron Density Server". Uppsala University. Retrieved 2013-04-06.
  17. ^ Kleywegt GJ, Harris MR, Zou JY, Taylor TC, Wählby A, Jones TA (Dec 2004). "The Uppsala Electron-Density Server". Acta Crystallogr D. 60 (Pt 12 Pt 1): 2240–2249. doi:10.1107/S0907444904013253. PMID 15572777.
  18. ^ 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.
  19. ^ "Content Growth Report". RCSB PDB. Retrieved 2013-04-06.
  20. ^ wwPDB.org. "wwPDB: 2013 News". wwpdb.org.
  21. ^ wwPDB.org. "wwPDB: 2019 News". wwpdb.org.
  22. ^ Westbrook J, Ito N, Nakamura H, Henrick K, Berman HM (April 2005). "PDBML: the representation of archival macromolecular structure data in XML" (PDF). Bioinformatics. 21 (7): 988–992. doi:10.1093/bioinformatics/bti082. PMID 15509603.
  23. ^ "ICM-Browser". Molsoft L.L.C. Retrieved 2013-04-06.
  24. ^ "Swiss PDB Viewer". Swiss Institute of Bioinformatics. Retrieved 2013-04-06.
  25. ^ "STAR: Biochem - Home". web.mit.edu.
  26. ^ "VisProt3DS". Molecular Systems Ltd. Retrieved 2013-04-06.

External links

  • The Worldwide Protein Data Bank (wwPDB) — parent site to regional hosts (below)
    • RCSB Protein Data Bank (USA)
    • PDBe (Europe)
    • PDBj (Japan)
    • BMRB, Biological Magnetic Resonance Data Bank (USA)
  • wwPDB Documentation — documentation on both the PDB and PDBML file formats
  • Looking at Structures — The RCSB's introduction to crystallography
  • PDBsum Home Page — Extracts data from other databases about PDB structures.
  • Nucleic Acid Database, NDB — a PDB mirror especially for searching for nucleic acids
  • Introductory PDB tutorial sponsored by PDB
  • PDBe: Quick Tour on EBI Train OnLine
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