Dear all,
The standardization of protein modification handling ensures that there
is a single correct approach to handling each protein modification that
occurs within the PDB archive. However, there are many existing PDB
entries that contain protein modifications which do not follow these
handling conventions.
As part of the protein modifications remediation project, all model
coordinates files containing protein modifications are being re-released
to add a new protein modification data category. This new category will
list all observed PCMs/PTMs within the entry, as well as their type and
category, allowing better findability.
A new category will also be added to the Chemical Component Definition
(CCD) files. It will state whether the CCD is a known PCM, its type and
category, as well as on which positions in the amino acid and in the
polypeptide it is expected to be observed. If this PCM is also a known
PTM, it will have the Uniprot generic PTM accession ID.
Finally, any protein modifications that are inconsistently handled
within a PDB entry will be amended, to ensure that a given modification
is consistently handled in the PDB archive.
Detailed information about this work is available from GitHub, including
PDBx/mmCIF dictionary extension and a set of example files, and complete
documentation of the additional annotation:
https://github.com/wwPDB/protein-modification-extension
Questions or feedback? Contact deposit-h...@mail.wwpdb.org.
The protein chemical modifications (PCMs) and post translational
modifications (PTMs) remediation project is a wwPDB collaborative
project carried out principally by PDBe at EMBL-EBI, and is funded by
BBSRC grant number BB/V018779/1.
Read this news online
<https://www.wwpdb.org/news/news?year=2024#662fa1a565d8a8cacaf76f9c>
Kind regards,
Deborah Harrus, on behalf of the wwPDB
--
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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