wwPDB Statement on Retraction of PDB Entries

In its December 4, 2009 issue, the Journal of Biological Chemistry (JBC) retracted an article by H.M. Krishna Murthy et al. describing a structure of the Dengue Virus NS3 serine protease published 10 years earlier (http://www.jbc.org/content/284/49/34468.full). Thereafter, the Editor of JBC requested that the Protein Data Bank (PDB) entry described in that paper (PDB ID 1BEF) be removed from the archive (Status: Obsolete). This request was implemented immediately.

It is the current policy of the Worldwide PDB (wwPDB) that PDB archival entries can be made obsolete following a request from the people responsible for publishing it (be it the principal author or journal editors). Typically, authors themselves request an entry to be made obsolete because they have collected better experimental data or produced an improved interpretation of the existing data. In addition, the employer of an author may request entry removal, but in that case the request must be fully documented and a retraction published in the journal that published the original paper describing the entry. This policy mirrors the manner in which Bell Labs/Lucent Technologies handled the case of its employee J.H. Schon (http://en.wikipedia.org/wiki/Jan_Hendrik_Schon). It aims to ensure both due process for the depositor and the integrity of the global macromolecular structure archive.

In December 2009, the University of Alabama at Birmingham (UAB) announced on its website (http://www.uab.edu/reporterarchive/71570-uab-statement-on-protein-data-bank-issues) that it planned to retract 12 PDB entries and 10 papers (including the JBC publication described above; Table 1).

Subsequently, in line with policy, the wwPDB made PDB entries 1CMW, 1DF9, and 2GID obsolete when the corresponding papers were retracted by the journals.

As of mid-February 2015, 8 of the 12 PDB entries in question (Table 1) remained in the archive.

Per wwPDB policy, these entries will be obsoleted when one or more of the following events occur:

  1. The authors retract the publication and request that the PDB entry be obsoleted;
  2. The journals retract the publication; or
  3. There is a formal ruling of scientific misconduct from the US Department of Health and Human Services Office of Research Integrity (ORI, http://ori.hhs.gov). N.B.: The ORI neither publicizes the names of those under investigation nor comments on ongoing investigations.

The PDB is a historical archive that stores, annotates, and disseminates structure models and their related experimental data (deposition of which has been mandatory since February 2008). The wwPDB has convened expert, community-driven Validation Task Forces for X-ray (in 2008), NMR (in 2009), and (in collaboration with the EMDataBank) Cryo-EM (in 2010) to advise on the most suitable criteria to use for validating structure entries (model, experimental data, and fit of model to data) when they are deposited. Recommendations of these task forces are being implemented as part of a collaborative effort to unify the deposition, annotation, and validation procedures among the current wwPDB partners.

The results of these wwPDB validation procedures are captured in a report that is provided to depositors and can be transmitted by them to the journal to which the corresponding manuscript is submitted. Availability of such a report greatly facilitates assessment of the reliability of structural data and its interpretation by journal editors and referees alike. The wwPDB has urged journals publishing structural data on biological macromolecules to require submission of the wwPDB validation report together with the manuscript. The continuing mission of the wwPDB partners is to safeguard the integrity and improve the quality of the structural archive, with the support of the international structural biology community.

The Worldwide Protein Data Bank (wwPDB; http://wwpdb.org/) includes organizations that act as deposition, data processing, and distribution centers for PDB data. Current members are the RCSB PDB (USA), PDBe (Europe), PDBj (Japan), and the BMRB (USA). The mission of the wwPDB is to maintain a single Protein Data Bank archive of macromolecular structural data that is freely and publicly available to the global community.


Table 1. PDB entries reviewed at the request of UAB.

PDB ID Status Citation
1BEF Obsolete Correction to Murthy et al. (2009) Journal of Biological Chemistry 284, 34468 doi: 10.1074/jbc.A005573200
1CMW Obsolete Retraction of articles by H. M. Krishna Murthy et al. (2010) Acta Cryst. D66, 222 doi: 10.1107/S0907444910000259
1DF9 Obsolete Retracted: Crystal structure of dengue virus NS3 protease in complex with a Bowman-Birk inhibitor: Implications for flaviviral polyprotein processing and drug design (2000) J. Mol. Biol. 301, 759-767 doi: 10.1006/JMBI.2000.3924
2QID Obsolete
1G40 Released Crystal structure of a complement control protein that regulates both pathways of complement activation and binds heparan sulfate proteoglycans (2001) Cell 104, 301-311 doi: 10.1016/S0092-8674(01)00214-8
1G44 Released
1L6L Released Structures of apolipoprotein A-II and a lipid-surrogate complex provide insights into apolipoprotein-lipid interactions (2002) Biochemistry 41, 11681-11691 doi: 10.1021/BI026069W
2OU1 Released
1RID Released Structure of vaccinia complement protein in complex with heparin and potential implications for complement regulation (2004) Proc. Natl. Acad. Sci. USA 101, 8924-8929 doi: 10.1073/PNAS.0400744101
1Y8E Released Structural basis for antagonism by suramin of heparin binding to vaccinia complement protein (2005) Biochemistry 44, 10757-10765 doi: 10.1021/bi050401x
2A01 Released Crystal structure of human apolipoprotein A-I: Insights into its protective effect against cardiovascular diseases (2006) Proc. Natl. Acad. Sci. USA 103, 2126-2131 doi: 10.1073/pnas.0506877103
2HR0 Released The structure of complement C3b provides insights into complement activation and regulation (2006) Nature 444, 221-225 doi: 10.1038/nature05258

First published on December 17, 2009

Updated February 2, 2010 and February 20, 2015

For additional information, see Safeguarding the integrity of protein archive (2010) Nature 463, 425 doi: 10.1038/463425c.