Protein Data Bank

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Protein Data Bank
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The Protein Data Bank (PDB) is a repository for the three-dimensional 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,[1] PDBj,[2] and RCSB[3]). 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.[4]

History[edit]

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.[5] SEARCH was instrumental in enabling networking, thus marking the functional beginning of the PDB.

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,[6] the PDB was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB);[7] the transfer was completed in June 1999. The new director was Helen M. Berman of Rutgers University (one of the member institutions of the RCSB).[8] 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[9] 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.[10] The data are then automatically checked for plausibility (the source code[11] for this validation software has been made available to the public at no charge).

Contents[edit]

The PDB database is updated weekly (UTC+0 Wednesday). Likewise, the PDB holdings list[12] is also updated weekly. As of 1 April 2014, the breakdown of current holdings is as follows:

Experimental
Method
Proteins Nucleic Acids Protein/Nucleic Acid
complexes
Other Total
X-ray diffraction 81972 1516 4263 4 87755
NMR 9093 1079 205 7 10384
Electron microscopy 517 52 171 0 740
Hybrid 59 3 2 1 65
Other 155 4 6 13 178
Total: 91796 2654 4647 25 99122
77,307 structures in the PDB have a structure factor file.
7,698 structures have an NMR restraint file.
1,454 structures in the PDB have a chemical shifts file.
700 structures in the PDB have a 3DEM map file.

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".[13][14]

Growth trend[edit]

In the past, the number of structures in the PDB has grown at an approximately exponential rate.[15] However, since 2007, the rate of accumulation of new proteins appears to have plateaued:

Number of searchable structures per year
Year # added Total
2013 9622 96,585
2012 8930 86,964
2011 8072 78,111
2010 7897 70,039
2009 7380 62,142
2008 6956 54,762
2007 7198 47,806
2006 6473 40,608
2005 5359 34,135
2004 5180 28,776
2003 4167 23,596
2002 3001 19,429
2001 2831 16,428
2000 2627 13,597
1999 2360 10,970
1998 2057 8,610
1997 1565 6,553
1996 1172 4,988
1995 945 3,816
1994 1289 2,871
1993 696 1,582
1992 192 886
1991 187 694
1990 142 507
1989 74 365
1988 53 291
1987 25 238
1986 18 213
1985 20 195
1984 22 175
1983 36 153
1982 32 117
1981 16 85
1980 16 69
1979 11 53
1978 6 42
1977 23 36
1976 13 13
1975 0 0
1974 0 0
1973 0 0
1972 0 0

Note: searchable structures vary over time as some become obsolete and are removed from the database. Template:SVG Chart

File format[edit]

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.[16] 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.)

Viewing the data[edit]

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,[17] VMD, MDL Chime, Pymol, UCSF Chimera, Rasmol, Swiss-PDB Viewer,[18] StarBiochem[19] (a Java-based interactive molecular viewer with integrated search of protein databank), Sirius, and VisProt3DS[20] (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.

See also[edit]

References[edit]

  1. ^ a b PDBe Protein Data Bank in Europe
  2. ^ a b Welcome to PDBj - Home
  3. ^ http://www.rcsb.org/
  4. ^ 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. 
  5. ^ 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. 
  6. ^ 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. 
  7. ^ RCSB | Research Collaboratory for Structural Bioinformatics
  8. ^ "RCSB PDB Newsletter Archive". RCSB Protein Data Bank. 
  9. ^ BMRB - Biological Magnetic Resonance Bank
  10. ^ Curry E, Freitas A, 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 978-1-441-97664-2. 
  11. ^ PDB Validation Suite
  12. ^ "PDB Current Holdings Breakdown". RCSB. 
  13. ^ "The Uppsala Electron Density Server". Uppsala University. Retrieved 2013-04-06. 
  14. ^ Kleywegt GJ, Harris MR, Zou JY, Taylor TC, Wählby A, Jones TA (Dec 2004). "The Uppsala Electron-Density Server". Acta Crystallogr D Biol Crystallogr 60 (Pt 12 Pt 1): 2240–2249. doi:10.1107/S0907444904013253. PMID 15572777. 
  15. ^ "Content Growth Report". RCSB PDB. Retrieved 2013-04-06. 
  16. ^ 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. 
  17. ^ "ICM-Browser". Molsoft L.L.C. Retrieved 2013-04-06. 
  18. ^ "Swiss PDB Viewer". Swiss Institute of Bioinformatics. Retrieved 2013-04-06. 
  19. ^ STAR: Biochem - Home
  20. ^ "VisProt3DS". Molecular Systems Ltd. Retrieved 2013-04-06. 

External links[edit]