Protein Data Bank
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| Description | Protein structure X-ray crystallography NMR Structure Determination |
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| Data format | PDB |
| Website | www.wwpdb.org, www.pdbe.org, www.rcsb.org/pdb, www.pdbj.org |
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| Miscellaneous |
The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. (See also crystallographic database). The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, and RCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP and CATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.[1]
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[edit] 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 Dr. Walter Hamilton at the Brookhaven National Laboratory, Dr. 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 Dr. Meyer's programs, SEARCH, enabled researchers to remotely access information from the database to study protein structures offline.[2] SEARCH was instrumental in enabling networking, thus marking the functional beginning of the PDB.
Upon Hamilton's death in 1973, Dr. Tom Koeztle took over direction of the PDB for the subsequent 20 years. In January 1994, Dr. Joel Sussman of Israel's Weizmann Institute of Science was appointed head of the PDB. In October 1998,[3] the PDB was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB); the transfer was completed in June 1999. The new director was Dr. Helen M. Berman of Rutgers University (one of the member institutions of the RCSB).[4] In 2003, with the formation of the wwPDB, the PDB became an international organization. The founding members are PDBe (Europe), RCSB(USA), and PDBj (Japan). The BMRB 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 annotates each submitted entry.[5] The data are then automatically checked for plausibility (the source code for this validation software has been made available to the public at no charge).
[edit] Contents
The PDB database is updated weekly (UTC+0 Wednesday). Likewise, the PDB Holdings List is also updated weekly. As of 4 September 2012[update], the breakdown of current holdings is as follows:
| Experimental Method |
Proteins | Nucleic Acids | Protein/Nucleic Acid complexes |
Other | Total |
|---|---|---|---|---|---|
| X-ray diffraction | 69232 | 1390 | 3506 | 3 | 74131 |
| NMR | 8381 | 1005 | 190 | 7 | 9583 |
| Electron microscopy | 311 | 22 | 120 | 0 | 453 |
| Hybrid | 45 | 3 | 2 | 1 | 51 |
| Other | 141 | 4 | 5 | 13 | 163 |
| Total: | 78110 | 2424 | 3823 | 24 | 84381 |
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- 63,555 structures in the PDB have a structure factor file.
- 6,890 structures have an NMR restraint file.
- 650 structures in the PDB have a chemical shifts file.
These data show that most structures are determined by X-ray diffraction, but about 15% 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", where the electron maps can be viewed.
In the past, the number of structures in the PDB has grown at an approximately exponential rate. However, since 2007, the rate of accumulation of new proteins appears to have plateaued:
| Year | # added |
|---|---|
| 2007 | 7263 |
| 2008 | 7073 |
| 2009 | 7448 |
| 2010 | 7971 |
| 2011 | 8120 |
[edit] 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, started to be phased in. An XML version of this format, called PDBML, was described in 2005.[6] The structure files can be downloaded in any of these three formats. 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.)
[edit] Viewing the data
The structure files may be viewed using one of several open source computer programs. Some other free, but not open source programs include ICM-Browser, VMD, MDL Chime, Pymol, UCSF Chimera, Rasmol, Swiss-PDB Viewer, StarBiochem (a Java-based interactive molecular viewer with integrated search of protein databank), Sirius, and VisProt3DS (a tool for Protein Visualization in 3D stereoscopic view in anaglyth and other modes). The RCSB PDB website contains an extensive list of both free and commercial molecule visualization programs and web browser plugins.
[edit] See also
- Crystallographic database
- Protein structure
- Protein structure databases
- PDBREPORT lists all anomalies (also errors) in PDB structures
- PDBsum — extracts data from other databases about PDB structures
- PDBWiki — a website for community annotation of PDB structures
- Proteopedia — a collaborative 3D encyclopedia of proteins and other molecules
[edit] References
- ^ Berman, H. M. (January 2008). "The Protein Data Bank: a historical perspective". Acta Crystallographica Section A: Foundations of Crystallography A64 (1): 88–95. doi:10.1107/S0108767307035623. PMID 18156675. http://journals.iucr.org/a/issues/2008/01/00/sc5004/sc5004.pdf.
- ^ 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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2143743/.
- ^ 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. http://nar.oxfordjournals.org/cgi/content/full/28/1/235.
- ^ "RCSB PDB Newsletter Archive". RCSB Protein Data Bank. http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/newsletters/newsletter.html.
- ^ Curry E, Freitas A, and O'Riáin S (2010). "The Role of Community-Driven Data Curation for Enterprises". In D. Wood. Linking Enterprise Data. Boston, MA: Springer US. pp. 25–47. ISBN 9781441976642. http://books.google.com/?id=DsMrnk9-4NsC&lpg=PA25&pg=PA25#v=onepage&q&f=false.
- ^ 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. http://bioinformatics.oxfordjournals.org/cgi/reprint/21/7/988.pdf.
[edit] 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
