The worldwide Protein Data Bank (wwPDB):
ensuring a single, uniform archive of PDB data
Helen Berman*, Kim Henrick1, Haruki Nakamura2and John L. Markley3
RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of
New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA,1MSD-EBI, EMBL Outstation-Hinxton, Cambridge
CB10 1SD, UK,2PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871,
Japan and3BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive,
Madison, WI 53706, USA
Received September 14, 2006; Accepted October 20, 2006
The worldwide Protein Data Bank (wwPDB) is the
international collaboration that manages the depo-
sition, processing and distribution of the PDB
archive. The online PDB archive is a repository for
the coordinates and related information for more
than 38000 structures, including proteins, nucleic
acids and large macromolecular complexes that
have been determined using X-ray crystallography,
NMR and electron microscopy techniques. The
founding members of the wwPDB are RCSB PDB
(USA), MSD-EBI (Europe) and PDBj (Japan) [H.M.
Berman, K. Henrick and H. Nakamura (2003) Nature
Struct. Biol., 10, 980]. The BMRB group (USA) joined
the wwPDB in 2006. The mission of the wwPDB is to
maintain a single archive of macromolecular struc-
tural data that are freely and publicly available to the
global community. Additionally, the wwPDB pro-
vides a variety of services to a broad community of
users. The wwPDB website at http://www.wwpdb.
org/ provides information about services provided
by the individual member organizations and about
projects undertaken by the wwPDB.
HISTORY AND BACKGROUND
The Protein Data Bank (PDB) was founded in 1971 to pro-
vide a repository for three-dimensional (3D) structure data
of experimentally determined biological macromolecules
(1–3). The PDB archive contains 3D coordinate data,
information about the chemical content such as polymer
sequence and ligand chemistry, information about the experi-
ment used to derive the structure and some qualitative
descriptions of the structure. When the PDB was in its
infancy, the archive contained seven structures composed of
loosely structured free text. Today, the PDB archive contains
close to 40000 structures and relies upon strict ontologies
that define the content of these entries.
The data contained in the PDB are generated and submitted
by scientists from around the globe to sites in the United
States, Europe and Asia. The worldwide PDB (wwPDB)
was established in 2003 to formally recognize the interna-
tional nature of the PDB archive (2,4) and to ensure that
the data files remain uniform in content and format. The
founding members are the RCSB PDB (USA) (1), the Macro-
molecular Structure Database at the European Bioinformatics
Institute (MSD-EBI) (5) and the Protein Data Bank Japan
(PDBj) at Osaka University. These wwPDB sites share
responsibilities in data deposition, processing and distribution
of the PDB archive, and agree to support a single, standard-
ized archive of structural data (Table 1). The BioMagRes-
Bank (BMRB) at the University of Wisconsin-Madison
(USA) (6) became a member in 2006 and will be a deposition
site for primary experimental data and PDB data.
A wwPDB Advisory Committee (wwPDBAC) consists of
representatives appointed by each member site as well as rep-
resentatives of the international X-ray, NMR and electron
microscopy (EM) communities. wwPDBAC meets yearly
and provides advice about policies governing the content,
format and distribution of the PDB data files.
The website (http://www.wwpdb.org/) contains the formal
agreement for the operation of the wwPDB organization,
links to the deposition and access sites, and news and
announcements about policies and projects related to the
MEMBER DEPOSITION SITES
The advances in protein cloning, expression, labeling, puri-
fication through to structure determination has resulted in a
rapid increase in the rate at which new protein structures
are determined. Progress is also being made in structure
determinations of nucleic acids, particularly RNA molecules.
A key component of the wwPDB is that its tools are able to
efficiently capture and curate data as the amount deposited
*To whom correspondence should be addressed. Tel: +1 732 445 4667; Fax: +1 732 445 4320; Email: email@example.com
? 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
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Published online 16 November 2006Nucleic Acids Research, 2007, Vol. 35, Database issueD301–D303
grows exponentially (Table 1). Although the sites are physi-
cally dispersed and use three different tools for data capture
and processing (ADIT, ADIT-NMR and AutoDep), all the
data are annotated and processed using common standards.
To ensure that the core data are represented uniformly, the
wwPDB sites actively collaborate to exchange core reference
information (e.g. the dictionary description for ligands) and to
ensure that standard practices are followed. The annotators at
all sites maintain daily communication via video teleconfer-
encing, exchange visits and email; they are currently extend-
ing and updating the annotation manuals that will be made
Every week, the data processed at each site are forwarded
to the RCSB PDB for inclusion in the archive. At present, the
RCSB PDB is the archive keeper and as such has sole write
access to the PDB archive.
Statistics about the PDB structures deposited and processed
by the wwPDB are available from http://www.wwpdb.org/
stats.html (Tables 2 and 3).
DATA ACCESS: MEMBER FTP AND WEBSITES
The ‘PDB archive’ is the collection of flat files that are
maintained in three different formats: the legacy PDB file
format; the PDB exchange format that follows the mmCIF
syntax (http://deposit.pdb.org/mmcif/); and the PDBML/XML
format (7) that is a direct translation of the PDB exchange for-
mat. Each wwPDB site distributes the same PDB archive via
FTP. The archive is updated weekly.
Time-stamped snapshots of the PDB archive are added
each year to ftp://snapshots.rcsb.org. They provide a frozen
copy of the archive as it appeared at that time for research
and historical purposes. The most recent snapshot was
added in January 2006. It includes the 34421 experimentally
determined coordinate files that were current (i.e. not obso-
lete) as of January 3, 2006, and the directory containing the
frozen content as of January 6, 2005. Scripts are available
to download all, or part, of a snapshot automatically.
In addition to providing access to the PDB archive, each
wwPDB site provides databases and websites that provide
different views and analyses of the structural data contained
within the PDB archive (8–14).
wwPDB members collaborate to ensure the uniformity of the
PDB archive. The PDB Exchange Dictionary consolidates
content from a variety of dictionaries and includes extensions
to describe NMR, EM and protein production data (15).
wwPDB data processing, exchange and annotation depend
upon this dictionary and the mmCIF format (16) to help
make the data more consistent across the archive.
In the past, query across the complete PDB archive has
been limited by missing, erroneous and inconsistently
reported data, nomenclature and functional annotation. The
evolution of experimental methods, functional knowledge
of proteins and methods used to process these data has intro-
duced various inconsistencies into the PDB archive and has
inspired different versions of the PDB format.
Over the years, the MSD-EBI, PDBj and the RCSB PDB
have been working individually on correcting errors in the
archive. Under the wwPDB banner, these groups are now
working to integrate all remediation efforts into a single con-
sistent collection of data files. This work includes improving
the representation of PDB small molecule data, assessing the
required chemical definitions and their correspondences in
PDB entries, resolving any remaining differences in the
macromolecular sequences assigned by each group and
resolving differences in primary citation assignments. The
BMRB has been collaborating with MSD-EBI and RCSB
PDB on standardizing restraint data associated with PDB
The remediated data (PDB V.2) will be made available
for public review in 2007 and will form the basis of the
wwPDB websites. The data released before remediation
(PDB V.1) will continue to be available for the historical
Table 1. wwPDB Data deposition and access sites
Access PDB FTPDeposit data Main website
Table 2. PDB structures deposited and processed by year and site (as of
August 28, 2006)
RCSB PDBPDBj EBIPDBj EBI
Table 3. PDB structures released per year (experimentally solved structures
only, as of August 28, 2006)
D302Nucleic Acids Research, 2007, Vol. 35, Database issue
PHASING OUT THEORETICAL MODEL Download full-text
DEPOSITIONS TO THE PDB ARCHIVE
Effective October 15, 2006, PDB depositions were restricted
to atomic coordinates that are substantially determined by
experimental measurements on specimens containing bio-
logical macromolecules. This policy was recommended and
endorsed by a working group composed of structural and
computational biologists and endorsed by the wwPDB Advi-
sory Committee. Thus, theoretical model depositions (such
as models determined purely in silico using, for example,
homology or ab initio methods) will no longer be accepted.
NEWS AND ANNOUNCEMENTS
The News sections of the wwPDB website gives information
about the outcome of the wwPDBAC meetings and policy
statements affecting the PDB data files. A recent example
is the announcement of the policy for the archiving of
in silico models (19).
The RCSB PDB is operated by Rutgers, The State University
of New Jersey and the San Diego Supercomputer Center and
the Skaggs School of Pharmacy and Pharmaceutical Sciences
at the University of California, San Diego. It is supported by
funds from the National Science Foundation, the National
Institute of General Medical Sciences, the Office of Science,
Department of Energy, the National Library of Medicine, the
National Cancer Institute, the National Center for Research
Resources, the National Institute of Biomedical Imaging and
Bioengineering, the National Institute of Neurological
Disorders and Stroke and the National Institute of Diabetes
and Digestive and Kidney Diseases. E-MSD gratefully
acknowledges the support
(GR062025MA), the EU (TEMBLOR, NMRQUAL and
IIMS), CCP4, the BBSRC, the MRC and EMBL. 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). The BMRB is
for this article was provided by the agencies supporting the
of the Wellcome Trust
Conflict of interest statement. None declared.
1. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N.,
Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data
Bank. Nucleic Acids Res., 28, 235–242.
2. Berman,H.M., Henrick,K. and Nakamura,H. (2003) Announcing the
worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.
3. Bernstein,F.C., Koetzle,T.F., Williams,G.J.B., Meyer,E.F.,Jr,
Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and
Tasumi,M. (1977) Protein Data Bank: a computer-based archival
file for macromolecular structures. J. Mol. Biol., 112,
4. Henrick,K., Berman,H.M. and Nakamura,H. (2005) The Protein Data
Bank and the wwPDB. In Jorde,L.B., Little,P.F.R., Dunn,M.J. and
Subramaniam,S. (eds), Encyclopedia of Genomics, Proteomics, and
Bioinformatics. John Wiley & Sons Ltd, Chichester, Vol. 7,
5. Golovin,A., Oldfield,T.J., Tate,J.G., Velankar,S., Barton,G.J.,
Boutselakis,H., Dimitropoulos,D., Fillon,J., Hussain,A., Ionides,J.M.
et al. (2004) E-MSD: an integrated data resource for bioinformatics.
Nucleic Acids Res., 32, D211–D216.
6. Ulrich,E.L., Markley,J.L. and Kyogoku,Y. (1989) Creation of a nuclear
magnetic resonance data repository and literature database. Protein
Seq. Data Anal., 2, 23–37.
7. Westbrook,J., Ito,N., Nakamura,H., Henrick,K. and Berman,H.M.
(2005) PDBML: the representation of archival macromolecular
structure data in XML. Bioinformatics, 21, 988–992.
8. Deshpande,N., Addess,K.J., Bluhm,W.F., Merino-Ott,J.C.,
Townsend-Merino,W., Zhang,Q., Knezevich,C., Xie,L., Chen,L.,
Feng,Z. et al. (2005) The RCSB Protein Data Bank: a redesigned query
system and relational database based on the mmCIF schema. Nucleic
Acids Res., 33, D233–D237.
9. Kouranov,A., Xie,L., de la Cruz,J., Chen,L., Westbrook,J.,
Bourne,P.E. and Berman,H.M. (2006) The RCSB PDB
information portal for structural genomics. Nucleic Acids Res.,
10. Tagari,M., Tate,J., Swaminathan,G.J., Newman,R., Naim,A.,
Vranken,W., Kapopoulou,A., Hussain,A., Fillon,J., Henrick,K. et al.
(2006) E-MSD: improving data deposition and structure quality.
Nucleic Acids Res., 34, D287–D290.
11. Henrick,K. and Thornton,J.M. (1998) PQS: a protein quarternary file
server. Trends Biochem. Sci., 23, 358–361.
12. Kinoshita,K. and Nakamura,H. (2004) eF-site and PDBjViewer:
database and viewer for protein functional sites. Bioinformatics, 20,
13. Standley,D.M., Toh,H. and Nakamura,H. (2005) GASH: an
improved algorithm for maximizing the number of equivalent
residues between two protein structures. BMC Bioinformatics,
14. Wako,H., Kato,M. and Endo,S. (2004) ProMode: a database of normal
mode analyses on protein molecules with a full-atom model.
Bioinformatics, 20, 2035–2043.
15. Westbrook,J., Yang,H., Feng,Z. and Berman,H.M. (2005) The use of
mmCIF architecture for PDB data management. In Hall,S.R. and
McMahon,B. (eds), International Tables for Crystallography. Springer,
Dordrecht, The Netherlands, Vol. G, pp. 539–543.
16. Fitzgerald,P.M.D., Westbrook,J.D., Bourne,P.E., McMahon,B.,
Watenpaugh,K.D. and Berman,H.M. (2005) Macromolecular
dictionary (mmCIF). In Hall,S.R. and McMahon,B. (eds), International
Tables for Crystallography. Springer, Dordrecht, The Netherlands, Vol.
G, pp. 295–443.
17. Doreleijers,J.F., Mading,S., Maziuk,D., Sojourner,K., Yin,L., Zhu,J.,
Markley,J.L. and Ulrich,E.L. (2003) BioMagResBank database with
sets of experimental NMR constraints corresponding to the structures
of over 1400 biomolecules deposited in the Protein Data Bank.
J. Biomol. NMR, 26, 139–146.
18. Doreleijers,J.F., Nederveen,A.J., Vranken,W., Lin,J., Bonvin,A.M.,
Kaptein,R., Markley,J.L. and Ulrich,E.L. (2005) BioMagResBank
databases DOCR and FRED containing converted and filtered sets of
experimental NMR restraints and coordinates from over 500 protein
PDB structures. J. Biomol. NMR, 32, 1–12.
19. Berman,H.M., Burley,S.K., Chiu,W., Sali,A., Adzhubei,A.,
Bourne,P.E., Bryant,S.H., Dunbrack,J.R.L., Fidelis,K., Frank,J. et al.
(2006) Outcome of a workshop on archiving structural models of
biological macromolecules. Structure, 14, 1211–1217.
Nucleic Acids Research, 2007, Vol. 35, Database issue D303