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| Primary citation | PMID 30357364 |
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| Data format | mmCIF,PDB |
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TheProtein Data Bank (PDB)[1] is adatabase for the three-dimensional structural data of large biological molecules such asproteins andnucleic acids, which is overseen by theWorldwide Protein Data Bank (wwPDB). This structural data is obtained and deposited bybiologists andbiochemists worldwide through the use of experimental methodologies such asX-ray crystallography,NMR spectroscopy, and, increasingly,cryogenic electron microscopy. All submitted data are reviewed by expertbiocurators 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 ofstructural biology, such asstructural 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 andCATH classify protein structures, whilePDBsum provides a graphic overview of PDB entries using information from other sources, such asGene Ontology.[8][9]
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, theBrookhaven RAster Display (BRAD), to visualize these protein structures in 3-D. In 1969, with the sponsorship of Walter Hamilton at theBrookhaven 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 inNature New Biology[11] as a joint venture betweenCambridge 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'sWeizmann Institute of Science was appointed head of the PDB. In October 1998,[12]the PDB was transferred to theResearch Collaboratory for Structural Bioinformatics (RCSB);[13] the transfer was completed in June 1999. The new director wasHelen M. Berman ofRutgers University (one of the managing institutions of the RCSB, the other being theSan Diego Supercomputer Center atUC 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] TheBiological Magnetic Resonance Data Bank (BMRB)[6] joined in 2006. TheElectron Microscopy Data Bank (EMDB)[15] joined in 2021. Each of the five members ofwwPDB 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).
The PDB database is updated weekly (UTC+0 Wednesday), along with its holdings list.[18] As of 10 January 2023[update], the PDB comprised:
| Experimental Method | Proteins only | Proteins with oligosaccharides | Protein/Nucleic Acid complexes | Nucleic Acids only | Other | Oligosaccharides only | Total |
|---|---|---|---|---|---|---|---|
| X-ray diffraction | 152277 | 8969 | 8027 | 2566 | 163 | 11 | 172013 |
| NMR | 12104 | 32 | 281 | 1433 | 31 | 6 | 13887 |
| Electron microscopy | 9226 | 1633 | 2898 | 77 | 8 | 0 | 13842 |
| Hybrid | 189 | 7 | 6 | 12 | 0 | 1 | 215 |
| Neutron | 72 | 1 | 0 | 2 | 0 | 0 | 75 |
| Other | 32 | 0 | 0 | 1 | 0 | 4 | 309 |
| Total: | 173900 | 10642 | 11212 | 4091 | 202 | 22 | 200069 |
Most structures are determined by X-ray diffraction, but about 7% of structures are determined byprotein 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 adistance geometry problem. After 2013, a growing number of proteins are determined bycryo-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]
The file format initially used by the PDB was called the PDB file format. The original format was restricted by the width ofcomputer punch cards to 80 characters per line. Around 1996, the "macromolecular Crystallographic Information file" format, mmCIF, which is an extension of theCIF format was phased in. mmCIF became the standard format for the PDB archive in 2014.[22] In 2019, the wwPDB announced that depositions for crystallographic methods would only be accepted in mmCIF format.[23]
AnXML version of PDB, called PDBML, was described in 2005.[24]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 InternetURLs:
http://www.pdb.org/pdb/files/4hhb.pdb.gz orhttp://pdbe.org/download/4hhbhttp://www.pdb.org/pdb/files/4hhb.xml.gz orhttp://pdbe.org/pdbml/4hhbThe "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.)
The structure files may be viewed using one ofseveral free and open source computer programs, includingJmol,Pymol,VMD,Molstar andRasmol. Other non-free,shareware programs include ICM-Browser,[25]MDL Chime,UCSF Chimera, Swiss-PDB Viewer,[26] StarBiochem[27] (a Java-based interactive molecular viewer with integrated search of protein databank),Sirius, and VisProt3DS[28] (a tool for Protein Visualization in 3D stereoscopic view in anaglyph and other modes), andDiscovery Studio. The RCSB PDB website contains an extensive list of both free and commercial molecule visualization programs and web browser plugins.
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