SIFTS Mapping for UniProt sequences and PDB
Structures
SIFTS (Structure Integration with Function,
Taxonomy and Sequences) is a database of residue-level mappings
between UniProt protein sequences, and protein structures found in
the PDB. The database is updated for each PDB release, and is
provided by the PDBe
at EMBL-EBI.
When Jalview imports PDB data for a protein sequence found in UniProt, either via the 'View 3D Structure...' option, or the 'Fetch DB Refs' web services menu, Jalview will also download its SIFTS record and use that information to construct a mapping between the sequence and downloaded structure.
If, for some reason, no SIFTS mapping data exists, then Jalview will generate a mapping using its built-in Needleman and Wunsch global alignment algorithm. This method of mapping was used for all structures prior to version 2.10.
Controlling and troubleshooting SIFTS mappings
Configuration options controlling whether SIFTS mappings are used
can be found in the Tools → Preferences →
Structure tab, under 'Sequence ↔ Structure method'.
Note:
Changing the configuration will only affect how new mappings are
created. In order to recompute mappings for structures already
loaded, please reload the sequence & structural data.
Multi-Chain Mappings
SIFTS gives Jalview the
ability to display multi-chain mappings between UniProt sequences
and PDB structure data. This is important when working with
multimeric proteins, since the biological unit will contain several
structures for the same protein sequence. Multi-chain mapping allows
all residues in a structure to be located in the alignment, and
also, when shading the structure by sequence colours, enables
conservation patterns between oligomer interfaces to be explored.
To see this in action, load uniprot sequence for FER1_MAIZE then veiw PDB structure for 3B2F, you will notice that mousing over the sequence results to two positions being highlighted in the structure, also colouring the sequence transfers the color to all the mapped chains in the structure.
Viewing Mapping Output
The mapping provided
by the SIFTS record is accessible via File →
View mapping menu of the structure viewers. The screenshot below
is the mapping output for the {FER1_MAIZE ↔
3B2F} example described above, and confirms that all two chains
were mapped. The mapping method used can be seen within the area
highlighted with red boarder.
SIFTS Mapping integration was added in Jalview 2.10