The Protein Data Bank (PDB) is a
database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases sp ...
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 residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
s and
nucleic acid
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cl ...
s. The data, typically obtained by
X-ray crystallography
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...
,
NMR spectroscopy
Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fiel ...
, or, increasingly,
cryo-electron microscopy
Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample sol ...
, and submitted 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 from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe,
PDBj,
RCSB, and BMRB
). The PDB is overseen by an organization called the
Worldwide Protein Data Bank
The Worldwide Protein Data Bank, wwPDB, is an organization that maintains the archive of macromolecular structure. Its mission is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly availa ...
, wwPDB.
The PDB is a key in areas of
structural biology
Structural biology is a field that is many centuries old which, and as defined by the Journal of Structural Biology, deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every le ...
, such as
structural genomics
Structural genomics seeks to describe the 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 experimental and modeling ...
. 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 designa ...
and
CATH
The CATH Protein Structure Classification database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains. It was created in the mid-1990s by Professor Christine Orengo and coll ...
classify protein structures, while
PDBsum
PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank. The original version of the database was developed around 1995 by Roman Laskowski and collaborators at Universi ...
provides a graphic overview of PDB entries using information from other sources, such as
Gene ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and g ...
.
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 Brookhaven may refer to:
Places Canada
* Amesbury, Toronto, also known as Brookhaven-Amesbury, a Toronto neighbourhood
United States
* Brookhaven, Georgia, a city just northeast of Atlanta
** Brookhaven/Oglethorpe (MARTA station), a passenger rail ...
(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 laboratory located in Upton, Long Island, and was formally established in 1947 at the site of Camp Upton, a former U.S. Army base and Japanese internment c ...
, Edgar Meyer (
Texas A&M University
Texas A&M University (Texas A&M, A&M, or TAMU) is a public, land-grant, research university in College Station, Texas. It was founded in 1876 and became the flagship institution of the Texas A&M University System in 1948. As of late 2021, T ...
) 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
''Nature'' is a British weekly scientific journal founded and based in London, England. As a multidisciplinary publication, ''Nature'' features peer-reviewed research from a variety of academic disciplines, mainly in science and technology. ...
as a joint venture between
Cambridge Crystallographic Data Centre
The Cambridge Crystallographic Data Centre (CCDC) is a non-profit organisation based in Cambridge, England. Its primary activity is the compilation and maintenance of the Cambridge Structural Database, a database of small molecule crystal struc ...
, 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
Joel L. Sussman (born September 24, 1943) is an Israeli crystallographer best known for his studies on acetylcholinesterase, a key protein involved in transmission of nerve signals. He is the Morton and Gladys Pickman Professor of Structural Bio ...
of Israel's
Weizmann Institute of Science
The Weizmann Institute of Science ( he, מכון ויצמן למדע ''Machon Vaitzman LeMada'') is a public research university in Rehovot, Israel, established in 1934, 14 years before the State of Israel. It differs from other Israeli unive ...
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
Helen Miriam Berman is a Board of Governors Professor of Chemistry and Chemical Biology at Rutgers University and a former director of the RCSB Protein Data Bank (one of the member organizations of the Worldwide Protein Data Bank). A structural b ...
of
Rutgers University
Rutgers University (; RU), officially Rutgers, The State University of New Jersey, is a Public university, public land-grant research university consisting of four campuses in New Jersey. Chartered in 1766, Rutgers was originally called Queen's ...
(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 (UCSD). SDSC is located at the UCSD campus' Eleanor Roosevelt College east end, immediately north the Hopkins Parking Structure. ...
at
UC San Diego
The University of California, San Diego (UC San Diego or colloquially, UCSD) is a public university, public Land-grant university, land-grant research university in San Diego, California. Established in 1960 near the pre-existing Scripps Insti ...
). 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 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:
::134,146 structures in the PDB have a
structure factor
In condensed matter physics and crystallography, the static structure factor (or structure factor for short) is a mathematical description of how a material scatters incident radiation. The structure factor is a critical tool in the interpretation ...
file.
::10,289 structures have an NMR restraint file.
::4,814 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.
::4,718 structures in the PDB have a
3DEM
Transmission electron cryomicroscopy (CryoTEM), commonly known as cryo-EM, is a form of cryogenic electron microscopy, more specifically a type of transmission electron microscopy (TEM) where the sample is studied at cryogenic temperatures (genera ...
map file deposited in
EM Data Bank The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformat ...
Most structures are determined by X-ray diffraction, but about 10% 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 Distance geometry is the branch of mathematics concerned with characterizing and studying sets of points based ''only'' on given values of the distances between pairs of points. More abstractly, it is the study of semimetric spaces and the isome ...
problem. After 2013, a growing number of proteins are determined by
cryo-electron microscopy
Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample sol ...
. Clicking on the numbers in the linked external table displays examples of structures determined by that method.
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 is stored on the "electron density server".
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, and 100,000 in 2014.
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 arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. T ...
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 termed as a web address, is a reference to a web resource that specifies its location on a computer network and a mechanism for retrieving it. A URL is a specific type of Uniform Resource Identifie ...
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 chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry.
It is written in the ...
,
Pymol
PyMOL is an open source but proprietary 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 ...
,
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. It was originally developed by Roger Sayle ...
. 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
MDL ''Chime'' was a free plugin used by web browsers to display the three-dimensional structures of molecules. and was based on the RasMol code.
Chime was used by a wide range of biochemistry web sites for the visualization of macromolecules ...
,
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, a ...
, Swiss-PDB Viewer, StarBiochem (a Java-based interactive molecular viewer with integrated search of protein databank),
Sirius
Sirius is the list of brightest stars, brightest star in the night sky. Its name is derived from the Ancient Greek language, Greek word , or , meaning 'glowing' or 'scorching'. The star is designated α Canis Majoris, Latinisation ...
, 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 bDassault Systemes BIOVIA(formerly Accelrys).
The product suite has a stronacademic collaboration programme supporting ...
. The RCSB PDB website contains an extensive list of both free and commercial molecule visualization programs and web browser plugins.
See also
*
Crystallographic database A crystallographic database is a database specifically designed to store information about the structure of molecules and crystals. Crystals are solids having, in all three dimensions of space, a regularly repeating arrangement of atoms, ions, or ...
*
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, the monomers of the polymer. A single amino acid monomer ma ...
*
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 secondary and tertiary structure from primary structure. Structure prediction is different ...
*
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
PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank. The original version of the database was developed around 1995 by Roman Laskowski and collaborators at Universi ...
—extracts data from other databases about PDB structures
*
Proteopedia
Proteopedia is a wiki, 3D encyclopedia of proteins and other molecules.
The site contains a page for every entry in the Protein Data Bank (>130,000 pages), as well as pages that are more descriptive of protein structures in general such as acetylch ...
—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(USA)
*
PDBe(Europe)
*
PDBj(Japan)
*
BMRB, Biological Magnetic Resonance Data Bank(USA)
€”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 PDBPDBe: Quick Tour on EBI Train OnLine
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