Dear all,
The PDB archive is now including annotation of protein chemical
modifications (PCMs) and post-translational modifications (PTMs) in a
standardized way.
As previously announced
<https://www.wwpdb.org/news/news?year=2024#662fa1a565d8a8cacaf76f9c>,
thePDBx/mmCIF dictionary
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/>has been
extended to enhance PCM and PTM annotation.
This includes new PDBx/mmCIF categories and items as follows:
In the Chemical Component Definition (CCD) files:
* A new item in thechem_comp
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/chem_comp.html>category:chem_comp.pdbx_pcm
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_chem_comp.pdbx_pcm.html>,
stating whether the CCD is a known PCM/PTM.
* A new category calledpdbx_chem_comp_pcm
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_chem_comp_pcm.html>,
stating the PCM/PTMtype
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_pcm.type.html>andcategory
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_chem_comp_pcm.category.html>,
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 PTM accession ID.
In the atomic coordinate files:
* A new item in thepdbx_entry_details
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_entry_details.html>category:pdbx_entry_details.has_protein_modification
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_pdbx_entry_details.has_protein_modification.html>,
stating if the entry contains a PCM/PTM.
* A new category calledpdbx_modification_feature
<https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_modification_feature.html>,
providing an instance-level annotation of all observed PCMs/PTMs
within the entry, as well as their type and category.
Additionally to providing this new annotation, any protein modifications
that are inconsistently handled within PDB entries are amended, to
ensure that a given modification is consistently handled in the PDB
archive. This includes a major clean-up of incorrect link records
(struct_conn).
All entries containing protein modifications are being re-released
gradually from October 2024, throughout Spring 2025.
This standardization ensures that there is a single approach to handling
each protein modification that occurs within the PDB archive, allowing
better findability.
Questions or feedback? contactdeposit-h...@mail.wwpdb.org.
The protein chemical modifications (PCMs) and post translational
modifications (PTMs) remediation project is a wwPDB collaborative
project carried out principally byPDBe
<https://www.ebi.ac.uk/pdbe/>atEMBL-EBI <https://www.ebi.ac.uk/>, and is
funded by BBSRC grant number BB/V018779/1.
Kind regards,
Deborah Harrus, on behalf of the wwPDB
--
-------------------------------------------------------------------
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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