UniProt release 13.6
Published July 1, 2008
Transient pleasures of the mind
Symmetry and round objects, including round numbers, easily fascinate the human mind. Thus, UniProtKB is happy to announce that we have a double set of round numbers to celebrate: UniProtKB/Swiss-Prot now contains over 50'000 cross-references to PDB and over 5'000 mammalian entries with experimental 3D-structures.
It is deeply satisfactory to see the 3D-structure of a protein. 3D-structures show the interactions between proteins and other macromolecules, and between proteins and small ligands, such as metal ions, substrates and inhibitors. Determining the 3D-structure is an important step for elucidating the mode of action of a well-characterized protein, and it provides a starting point for the classification of an uncharacterized protein and the prediction of its physiological role.
UniProtKB provides access to protein 3D-structures via cross-references to PDB (see for example P00734). The number of structures is constantly increasing, and quite frequently several structures have been determined for a given protein. Thus, the 50'000 cross-references to PDB in UniProtKB/Swiss-Prot correspond to more than 12'700 individual entries. Over 5'000 of these (about 40%) are from mammalian model organisms, including close to 3'300 human entries, while bacteria and archaea account for over 4'500 of the entries with links to PDB. Escherichica coli strain K12 is currently the best studied organism at the structural level, with 1035 out of its 4'339 proteins (almost 25%) having at least one link to a PDB entry. Close to 6'000 additional links to PDB are in UniProtKB/TrEMBL, corresponding to another 3'500 entries.
Thanks to the efforts of individual laboratories and structural proteomics groups, the number of experimental 3D-structures is rapidly increasing, and so the symmetrical roundness of the present numbers is a very transient phenomenon. Soon for every new protein there may be a family member with an experimental 3D-structure, even for membrane proteins. That is definitely something to look forward to.
Cross-references to AGRICOLA
In the flat file, the RX (Reference cross-reference) line is an optional line which is used to indicate cross-references to bibliographic databases. We have introduced cross-references to AGRICOLA, the National Agricultural Library's catalog of citations to agricultural literature. The valid bibliographic database names and their associated identifiers are now:
|MEDLINE||Eight-digit MEDLINE Unique Identifier (UI)|
|PubMed||PubMed Unique Identifier (PMID)|
|DOI||Digital Object Identifier (DOI)|
|AGRICOLA||AGRICOLA Unique Identifier|
Q01901: RX AGRICOLA=IND20450567;
Changes concerning keywords