[wwPDB] Improve Your Previously-Released Coordinates AND Keep Your Original PDB ID: Phase II

We are pleased to announce that from February 18, 2020 authors (PIs) of released PDB structures can update the model coordinates while retaining the same PDB accession code, thereby preserving the link with the original publication. In this second and final phase of the project we have extended the versioning functionality to structures deposited prior to the roll out of OneDep--the common wwPDB system for deposition, validation, and biocuration.

For entries deposited via OneDep, depositors should log into the corresponding session at deposit.wwpdb.org and submit the request via the OneDep communication panel. For entries deposited via legacy systems, requests should be initiated by sending an email to deposit-help@mail.wwpdb.org and including the PDB code in the subject and body of the email. Once submitted, the revised model will be processed by wwPDB biocurators and the updated version released immediately upon depositor’s approval. Versioning of PDB entries will be limited to changes in the coordinate files, with no changes permitted to the deposited experimental data. To limit the impact on the wwPDB biocuration resources, PDB versioning is currently restricted to one replacement per PDB entry per year, and three entries per Principal Investigator per year. We will review this restriction in 2021.

The most recent version of the entry will be made available in the PDB archive FTP (ftp.wwpdb.org). All major versions of a PDB structure will be retained in the versioned FTP archive (ftp-versioned.wwpdb.org)--more information can be found on the wwPDB website. The structure of the versioned FTP archive has been built allowing for future extension of the PDB code format. PDB entry 1abc would therefore be found in the folder pdb_00001abc.

Changes made to entries during versioning are considered to be either major or minor. Updates to atomic coordinates, polymer sequence, or chemical description trigger a major version increment, while changes to any other categories are classified as minor. Changes introduced are recorded in the PDBx/mmCIF audit categories.

If you have any further queries regarding the process of PDB versioning, please contact the wwPDB at deposit-help@mail.wwpdb.org.

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