Data Deposition/Biocuration Services and Archive Management

In the first quarter of 2019, 3388 experimentally-determined structures were deposited to the archive. Data are processed by wwPDB partners RCSB PDB, PDBe, and PDBj.

89.7% were deposited with a release status of hold until publication; 6.6% were released as soon as annotation of the entry was complete; and 3.7% were held until a particular date.

83.7% of these entries were determined by X-ray crystallographic methods; 3.1% by NMR methods; and 13.0% by 3DEM.

During the same period, 2835 structures and 569 EMDB maps were released in the PDB.

Submission of PDBx/mmCIF format files for crystallographic depositions to the PDB will be mandatory from July 1st 2019 onward. PDB format files will no longer be accepted for deposition of structures solved by MX techniques.

PDBx/mmCIF will be the only format accepted for deposition of PDB structures resulting from macromolecular crystallography (MX), including X-ray, neutron, fiber, and electron diffraction methods via OneDep starting July 1st 2019. The deposition of PDBx/mmCIF format files will improve the efficiency of the deposition process and enhance validation through capture of the more extensive experimental metadata supported by PDBx/mmCIF, compared to the legacy PDB format. PDB entries with 100,000 or more atoms, and those with multiple character chain IDs are already not supported by the legacy PDB format. In addition, by 2021, we anticipate the PDB Chemical Component Identifier will need to be extended beyond three characters, which will necessarily result in full retirement of files in the PDB Core Archive that utilize the legacy PDB format.

Refmac, Phenix.refine, and Buster programs can now output PDBx/mmCIF formatted files. For users of other structure determination/refinement software packages, the wwPDB provides stand-alone and web-based tools to convert legacy PDB format files into PDBx/mmCIF format: pdb_extract and MAXIT. More information on outputting and preparing PDBx/mmCIF format files for deposition can be found on the wwPDB website.

The PDBx/mmCIF Working Group has committed to the PDBx/mmCIF data model. PDBx/mmCIF is also supported by visualization software applications, including Jmol/JSMol, LiteMol, Chimera, OpenRasMol, CCP4MG, COOT, PyMOL, VMD, MolMil, and NGL. In addition, other data resources, such as the Protein Model Portal and SASBDB, have adopted and extended the PDBx/mmCIF framework for data representation.

If you have any queries or comments regarding these changes, please contact the wwPDB consortium via deposit-help@mail.wwpdb.org.

In 2018, The Office of Research Integrity (ORI) of the U.S. Department of Health and Human Services announced their final Research Misconduct Finding in the case of H.M. Krishna Murthy. It was found that Murthy reported falsified and/or fabricated research in 10 journal publications and 12 corresponding PDB structures. While the ORI was gathering and evaluating evidence in this case, 5 Murthy structures in the PDB were obsoleted in accord with wwPDB policies, in response to retraction of 4 journal publications. Following a formal request from ORI, received on April 23rd 2018, the remaining 7 Murthy structures in the PDB were obsoleted, again in accord with wwPDB policies. ORI conduct within its investigations is designed to ensure due process for individuals accused of research misconduct, and strict confidentiality is maintained throughout. Only (the final?) findings of research misconduct are made public.

In December 2009, the University of Alabama at Birmingham (UAB) announced that it planned to retract 12 PDB entries and 10 related publications authored by H.M. Krishna Murthy, in his capacity as Principal Investigator and UAB employee. Following wwPDB review of structures at the request of UAB and in accord with wwPDB policy, 5 of the structures were obsoleted upon retraction of the related publications by the journals. Following wwPDB review of structures at the request of UAB and in accord with wwPDB policy, the remaining 7 structures were obsoleted upon receipt of the ORI request.

Since that time, all 5 publications associated with these 7 structures have been retracted by the journals. A detailed PDB history of this case is available.

RETRACTED: 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

Retraction of "Structures of Apolipoprotein A-II and a Lipid-Surrogate Complex Provide Insights into Apolipoprotein-Lipid Interactions" (2018) Biochemistry 57, 6044 doi: 10.1021/acs.biochem.8b00956

Retraction for Ganesh et al., Structure of vaccinia complement protein in complex with heparin and potential implications for complement regulation (2018) Proc Natl Acad Sci USA 115, E6965 doi: 10.1073/pnas.1806429115

Retraction of "Structural Basis for Antagonism by Suramin of Heparin Binding to Vaccinia Complement Protein" (2018) Biochemistry 57, 6043 doi: 10.1021/acs.biochem.8b00955

Retraction for Ajees et al., Crystal structure of human apolipoprotein A-I: Insights into its protective effect against cardiovascular diseases (2018) Proc Natl Acad Sci USA 115, E6966 doi: 10.1073/pnas.1806430115

RCSB PDB is looking for a Biochemical Information & Annotation Specialist to join the RCSB PDB team at Rutgers, The State University of New Jersey.

Deposition/Biocuration Services support Data Depositors who submit the results of their structural studies of biological macromolecules to the PDB. All data deposited undergo expert review. Each structure is examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources, and validated for scientific/technical accuracy.

Biocurators communicate daily with members of the deposition community, and annotate, publicly release, and update entries in the PDB archive.

For more information, see

wwPDB biocuration supporting open access to high-quality 3D structural biology data (2018) Database 2018: bay002 doi: 10.1093/database/bay002

The rewards of working as a data wrangler Science Careers doi: 10.1126/science.caredit.aaq0481

For more, visit our Careers page or Contact Us with questions.

Protein Data Bank: the single global archive for 3D macromolecular structure data describes the development of the PDB archive under wwPDB stewardship, such as new archival content, master format and dictionary, and major remediation efforts. The publication also emphasizes the importance of continued community interactions, the scientific and technical challenges the PDB faces, and charts the road ahead.

wwPDB consortium. (2019) Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res 47: D520-D528.