Protein Data Bank
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The Protein Data Bank (PDB) is a
database In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...
for the three-dimensional structural data of large biological molecules such as
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
s and
nucleic acid Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nuclei ...
s, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained and deposited by
biologist A biologist is a scientist who conducts research in biology. Biologists are interested in studying life on Earth, whether it is an individual Cell (biology), cell, a multicellular organism, or a Community (ecology), community of Biological inter ...
s and
biochemist Biochemists are scientists who are trained in biochemistry. They study chemical processes and chemical transformations in living organisms. Biochemists study DNA, proteins and Cell (biology), cell parts. The word "biochemist" is a portmanteau of ...
s worldwide through the use of experimental methodologies such as
X-ray crystallography X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract in specific directions. By measuring th ...
,
NMR spectroscopy Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique based on re-orientation of atomic nuclei with non-zero nuclear spins in an external magnetic f ...
, and, increasingly,
cryo-electron microscopy Cryogenic electron microscopy (cryo-EM) is a transmission electron microscopy technique applied to samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An ...
. All submitted data are reviewed by expert biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organizations (PDBe, PDBj, RCSB PDB, and BMRB). The PDB is a key in areas of
structural biology Structural biology deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries we ...
, such as
structural genomics Structural genomics seeks to describe the Protein Structure, 3-dimensional structure of every protein encoded by a given genome. This genome-based approach allows for a high-throughput method of structure determination by a combination of protein ...
. 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 A ( or ) was a poet as represented in Old English poetry. The scop is the Old English counterpart of the Old Norse ', with the important difference that "skald" was applied to historical persons, and scop is used, for the most part, to designat ...
and
CATH Cath may refer to: __NOTOC__ People * Cath Bishop (born 1971), British former rower and 2003 world champion * Cath Carroll (born 1960), British musician and music journalist * Cath Coffey (), one of the earliest members of British rap band Stereo ...
classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene Ontology.


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 Brookhaven National Laboratory (BNL) is a United States Department of Energy national laboratories, United States Department of Energy national laboratory located in Upton, New York, a hamlet of the Brookhaven, New York, Town of Brookhaven. It w ...
, Edgar Meyer (
Texas A&M University Texas A&M University (Texas A&M, A&M, TA&M, or TAMU) is a public university, public, Land-grant university, land-grant, research university in College Station, Texas, United States. It was founded in 1876 and became the flagship institution of ...
) 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. 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 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 The Weizmann Institute of Science ( ''Machon Weizmann LeMada'') is a Public university, public research university in Rehovot, Israel, established in 1934, fourteen years before the State of Israel was founded. Unlike other List of Israeli uni ...
was appointed head of the PDB. In October 1998, the PDB was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB); the transfer was completed in June 1999. The new director was Helen M. Berman of
Rutgers University Rutgers University ( ), officially Rutgers, The State University of New Jersey, is a Public university, public land-grant research university consisting of three campuses in New Jersey. Chartered in 1766, Rutgers was originally called Queen's C ...
(one of the managing institutions of the RCSB, the other being the
San Diego Supercomputer Center The San Diego Supercomputer Center (SDSC) is an organized research unit of the University of California, San Diego. Founded in 1985, it was one of the five original NSF supercomputing centers. Its research pursuits are high performance comput ...
at
UC San Diego The University of California, San Diego (UC San Diego in communications material, formerly and colloquially UCSD) is a public land-grant research university in San Diego, California, United States. Established in 1960 near the pre-existing Sc ...
). In 2003, with the formation of the wwPDB, the PDB became an international organization. The founding members are PDBe (Europe), RCSB (US), 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 annotate each submitted entry. 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).


Contents

The PDB database is updated weekly ( UTC+0 Wednesday), along with its holdings list. , the PDB comprised: ::162,041 structures in the PDB have a structure factor file. ::11,242 structures have an NMR restraint file. ::5,774 structures in the PDB have a
chemical shift In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of ...
s file. ::13,388 structures in the PDB have a 3DEM map file deposited in EM Data Bank Most structures are determined by X-ray diffraction, but about 7% of structures are determined by
protein NMR Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and ...
. 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 Cryogenic electron microscopy (cryo-EM) is a transmission electron microscopy technique applied to samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An ...
. 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.


File format

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. In 2019, the wwPDB announced that depositions for crystallographic methods would only be accepted in mmCIF format. An
XML Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing data. It defines a set of rules for encoding electronic document, documents in a format that is both human-readable and Machine-r ...
version of PDB, called PDBML, was described in 2005. 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
URL A uniform resource locator (URL), colloquially known as an address on the Web, is a reference to a resource that specifies its location on a computer network and a mechanism for retrieving it. A URL is a specific type of Uniform Resource Identi ...
s: * 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 Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. It is an open-source Java viewer for chemical structures in 3D. The name originated from ''Jva (the programming language) + olcules, and also the m ...
,
Pymol PyMOL is a source-available molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universall ...
, VMD, Molstar and
Rasmol RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank (PDB). History It was originally develo ...
. Other non-free,
shareware Shareware is a type of proprietary software that is initially shared by the owner for trial use at little or no cost. Often the software has limited functionality or incomplete documentation until the user sends payment to the software developer. ...
programs include ICM-Browser, MDL Chime,
UCSF Chimera UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories ...
, Swiss-PDB Viewer, StarBiochem (a Java-based interactive molecular viewer with integrated search of protein databank),
Sirius Sirius is the brightest star in the night sky. Its name is derived from the Greek word (Latin script: ), meaning 'glowing' or 'scorching'. The star is designated  Canis Majoris, Latinized to Alpha Canis Majoris, and abbr ...
, and VisProt3DS (a tool for Protein Visualization in 3D stereoscopic view in anaglyph and other modes), and
Discovery Studio Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. It is developed and distributed by Dassault Systemes BIOVIA (formerly Accelrys). The product suite has a strong academic collaboration programme, sup ...
. The RCSB PDB website contains an extensive list of both free and commercial molecule visualization programs and web browser plugins.


See also

* Crystallographic database *
Protein structure Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid ...
*
Protein structure prediction Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its Protein secondary structure, secondary and Protein tertiary structure, tertiary structure ...
*
Protein structure database In biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the ...
* PDBREPORT lists all anomalies (also errors) in PDB structures * PDBsum—extracts data from other databases about PDB structures * Proteopedia—a collaborative 3D encyclopedia of proteins and other molecules


References


External links


The Worldwide Protein Data Bank (wwPDB)
��parent site to regional hosts (below) *
RCSB Protein Data Bank
(US) *
PDBe
(Europe) *
PDBj
(Japan) *
BMRB, Biological Magnetic Resonance Data Bank
(US)

��documentation on both the PDB and PDBML file formats

—The RCSB's introduction to crystallography
PDBsum Home Page
��Extracts data from other databases about PDB structures.

��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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