In recognition of the growing international and interdisciplinary
nature of structural biology, three organizations have formed a
collaboration to oversee the newly formed worldwide Protein Data Bank
(wwPDB; www.wwpdb.org). The Research Collaboratory for Structural
Bioinformatics (RCSB), the Macromolecular Structure Database (MSD) at
the European Bioinformatics Institute (EBI) and the Protein Data Bank
Japan (PDBj) at the Institute for Protein Research in Osaka University
will serve as custodians of the wwPDB, with the goal of maintaining a
single archive of macromolecular structural data that is freely and
publicly available to the global community.
The wwPDB represents a milestone in the evolution of the Protein Data
Bank (PDB; www.pdb.org1, 2), which was established in 1971 at
Brookhaven National Laboratory as the sole international repository for
three-dimensional structure data of biological macromolecules. Since
July 1, 1999, the PDB has been managed by three member institutions of
the RCSB: Rutgers, The State University of New Jersey; the San Diego
Supercomputer Center at the University of California, San Diego; and
the Center for Advanced Research in Biotechnology of the National
Institute of Standards and Technology.
The wwPDB recognizes the importance of providing equal access to the
database?both in terms of depositing and retrieving data?from
different regions of the world. Therefore, the wwPDB members will
continue to serve as deposition, data processing, and distribution
sites. Deposition procedures will not be altered by the formation of
the wwPDB; data can still be deposited using ADIT at the RCSB and PDBj
or by using AutoDep at the EBI.
To ensure the consistency of PDB data, all entries will be validated
and annotated following a common set of criteria. All processed data
will be sent to the RCSB, which distributes the data worldwide. All
format documentation will be kept publicly available and the
distribution sites will mirror the PDB archive using identical
contents and subdirectory structure. However, each member of the
wwPDB will be able to develop its own Web site, with a unique view
of the primary data, providing a variety of tools and resources for
the global community.
An Advisory Board consisting of appointees from the wwPDB, the
International Union of Crystallography and the International Council
on Magnetic Resonance in Biological Systems will provide guidance
through annual meetings with the wwPDB consortium. This board is
responsible for reviewing and determining policy as well as providing
a forum for resolving issues related to the wwPDB. Specific details
about the Advisory Board can be found in the wwPDB charter, available
on the wwPDB Web site.
The RCSB is the 'archive keeper' of wwPDB. It has sole write access to
the PDB archive and control over directory structure and contents, as
well as responsibility for distributing new PDB identifiers to all
deposition sites. The PDB archive is a collection of flat files in the
legacy PDB file format3 and in the mmCIF4 format that follows the PDB
exchange dictionary (deposit.pdb.org/mmcif). This dictionary describes
the syntax and semantics of PDB data that are processed and exchanged
during the process of data annotation. It was designed to provide
consistency in data produced in structure laboratories, processed by
the wwPDB members and used in bioinformatics applications. The PDB
archive does not include the Web sites, browsers, software and database
query engines developed by researchers worldwide.
The members of the wwPDB will jointly agree to any modifications or
extensions to the PDB exchange dictionary. As data technology
progresses, other data formats (such as XML) and delivery methods may
be included in the official PDB archive if all the wwPDB members concur
on the alteration. Any new formats will follow the naming and
description conventions of the PDB exchange dictionary. In addition,
the legacy PDB format would not be modified unless there is a
compelling reason for a change. Should such a situation occur, all
three wwPDB members would have to agree on the changes and give the
structural biology community 90 days advance notice.
The creation of the wwPDB formalizes the international character of
the PDB and ensures that the archive remains single and uniform. It
provides a mechanism to ensure consistent data for software developers
and users worldwide. We hope that this will encourage individual
creativity in developing tools for presenting structural data, which
could benefit the scientific research community in general.
1. H.M. Berman, et al. (2000): Nucleic Acids Res. 28, pp. 235-242.
2. F.C. Bernstein, et al. (1977): J. Mol. Biol. 112, pp. 535-542 .
3. J. Callaway, et al. (1996): Protein Data Bank Contents Guide:
Atomic coordinate entry format description. (Brookhaven National
4. P.E. Bourne, H.M. Berman, K. Watenpaugh, J.D. Westbrook, &
P.M.D. Fitzgerald (1997): Methods Enzymol. 277, pp. 571-590.
The RCSB PDB is supported by funds from the National Science
Foundation, the Department of Energy, and the National Institutes of
Health. The MSD-EBI is supported by funds from the Wellcome Trust,
the European Union (TEMBLOR, NMRQUAL, SPINE, AUTOSTRUCT, and IIMS
awards), CCP4, the Biotechnology and Biological Sciences Research
Council (UK), the Medical Research Council (UK), and the European
Molecular Biology Laboratory. PDBj is supported by grant-in-aid from
the Institute for Bioinformatics Research and Development, Japan
Science and Technology Agency (BIRD-JST), and the Ministry of
Education, Culture, Sports, Science and Technology (MEXT).
H.M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980.
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.