For viral proteins, where a polyprotein is synthesized, and where the PDB entry contains all the components, the name polyprotein can be used.For example, if the UniProt name is insulin, the protein names correspond to the chain names: such as Insulin A chain and Insulin B chain. If the UniProt entry contains the complete gene sequence of a protein that is processed into more than one chain, the corresponding polypeptide name will be given as the name in the PDB entry.In the case of zymogens, if the UniProt name is "trypsinogen" but the activated protein is present in the structure, then "trypsin" is used as the name.If the author did indicate putative, then the wording will be retained. If the UniProt name refers to a precursor and the entry contains mature protein, the word precursor will not be included in the protein name.Protein molecule names and synonyms are standardized to be consistent with the corresponding UniProt entry and are listed in the _entity.pdbx_description and _entity_name_com.name records. Macromolecule information How are the macromolecule names and synonyms assigned? Protein molecule names are included in mixed case in the mmCIF format file to match the literature. Journal and entry author names that have the suffix "junior" will be represented as "Jr." and not as "junior", for example, ‘Smith Jr., J.’. If the author indicates that the entry will never be published, a journal name of 'not published' will be added to citation.journal_abbrev records. Patent IDs can be recorded (_citation.pdbx_database_id_patent), and the journal name will be ‘Patent’. When available, DOI numbers are also included. PubMed IDs are available for the primary citations of entries in the PDB, mmCIF and XML files. ThesisĬonference Proceedings and Thesis can only be included as primary citation, but not in secondary citations. The primary citation is the paper that describes the structure in the PDB entry. Citation informationĪuthors are encouraged to deposit their structures in advance of publication. If more than one PI is responsible for the entry, they will need to come to a mutual decision on the authorship. The authorship of the entry is at the discretion of the principal investigator (PI). Generally, at least one of the authors for the entry should be included in the author list for the primary citation. Alternatively, there may be more authors listed for the entry compared to the citation author. The authors for a PDB entry can be the same as the authors for the primary citation, or a subset of citation authors. PDB staff may modify the entry title during data processing or before entry release if the title is ambiguous or does not match the content of the structure.Īuthors may choose to suppress the information about the entry authors and title so that it does not appear on the PDB website until the entry is released to the public. Entry title, authors, and citation information Entry Title (_struct.title)Įntry titles should be descriptive and match the content of the entry. November 2021: IDs reserved for new ligand used in structure determination process.ġ. July 2021: major revision 4.0 to clarify content and provide examples in mmCIF format.
#INMR ADD STRUCTURE TO NMR UPDATE#
May 2018: Update biological assembly annotation procedure. November 2011: major revision 2.5, clarify content, update header list and UniProt sequence submission.Īugust 2017: Clarify Best representative conformer of NMR entries. March 2009: minor revision 2.3, updates on citation, header list, SITE records and added cif templates for structure factors.Īpril 2009: minor revision 2.4, update header list. The wwPDB staff will continue to update annotation practices in line with evolving structure determination and annotation methods.ĭecember 2008: Initial release as version 2.2 This document presents the current processing procedures. The version of the PDB file and its correspondence to the file format guide will be included in all files processed and released by the wwPDB. The processed entries follow the mmCIF format that complies with the PDB Exchange Dictionary (PDBx) Since 1999, the wwPDB has been responsible for processing PDB data with deposition centers at RCSB PDB, PDBe, and PDBj. Viral capsids and other complex assembliesġ5. Information specific to Electron Microscopy structuresġ4. Information specific to NMR structuresġ3. Information specific to X-ray structuresġ2. Polymer sequences and sequence database reference assignmentġ1. Entry title, authors, and citation informationģ. November 2021 Version 4.1 Table of Contents Prefaceġ. WwPDB Deposition Policies and wwPDB Biocuration Procedures Section B: wwPDB Biocuration Procedures
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