seqres.md

SEQRES and ATOM Records, Mapping to Uniprot (SIFTs)

How molecular sequences are linked to experimentally observed atoms.

Sequences and Atoms

In many experiments not all atoms that are part of the molecule under study can be observed. As such the ATOM records in PDB often contain missing atoms or only the part of a molecule that could be experimentally determined. In case of multi-domain proteins the PDB often contains only one of the domains (and in some cases even shorter fragments).

Let's take a look at an example. The Protein Feature View provides a graphical summary of the regions that have been observed in an experiment and are available in the PDB map to UniProt.

As you can see, there are three PDB entries (PDB IDs 3LOH, 2HR7, 3BU3) that cover different regions of the UniProt sequence for the insulin receptor.

The blue-boxes are regions for which atoms records are available. For the grey regions there is sequence information available in the PDB, but no coordinates.

Seqres and Atom Records

The sequence that has been used in the experiment is stored in the Seqres records in the PDB. It is often not the same sequence as can be found in Uniprot, since it can contain cloning-artefacts and modifications that were necessary in order to crystallize a structure.

The Atom records provide coordinates where it was possible to observe them.

    Seqres groups -> sequence that has been used in the experiment
    Atom groups   -> subset of Seqres groups for which coordinates could be obtained

The mmCIF/PDBx file format contains the information how the Seqres and atom records are mapped onto each other. However the PDB format does not clearly specify how to resolve this mapping. BioJava contains a utility class that maps the Seqres to the Atom records when parsing PDB files. This class performs an alignment using dynamic programming, which can slow down the parsing process. If you do not require the precise Seqres to Atom mapping, you can turn it off like this:

    AtomCache cache = new AtomCache();
            
    FileParsingParameters params = cache.getFileParsingParams();
            
    params.setAlignSeqRes(false);
            
    Structure structure = StructureIO.getStructure(...);
            

Accessing Seqres and Atom Groups

By default BioJava loads both the Seqres and Atom groups into the Chain objects.

    Chain   -> Seqres groups
            -> Atom groups

Groups that are part of the Seqres sequence as well as of the Atom records are mapped onto each other. This means you can iterate over all Seqres groups in a chain and check, if they have observed atoms.

Mapping from Uniprot to Atom Records

The mapping between PDB and UniProt changes over time, due to the dynamic nature of biological data. The PDBe has a project that provides up-to-date mappings between the two databases, the SIFTs project.

BioJava contains a parser for the SIFTs XML files. The SiftsMappingProvider also acts similar to the AtomCache class, that we discussed earlier and can automatically download and locally install SIFTs files.

Here, how to request the mapping for one particular PDB ID.

    List<SiftsEntity> entities = SiftsMappingProvider.getSiftsMapping("1gc1");
            
    for (SiftsEntity e : entities){
        System.out.println(e.getEntityId() + " " +e.getType());
        
        for ( SiftsSegment seg: e.getSegments()) {
            System.out.println(" Segment: " + seg.getSegId() + " " + seg.getStart() + " " + seg.getEnd()) ;
            
            for ( SiftsResidue res: seg.getResidues() ) {
                System.out.println("  " + res);
            }
        }
        
    }

This gives the following output:

    C protein
 Segment: 1gc1_C_1_181 1 181
  SiftsResidue [pdbResNum=1, pdbResName=LYS, chainId=C, uniProtResName=K, uniProtPos=26, naturalPos=1, seqResName=LYS, pdbId=1gc1, uniProtAccessionId=P01730, notObserved=false]
  SiftsResidue [pdbResNum=2, pdbResName=LYS, chainId=C, uniProtResName=K, uniProtPos=27, naturalPos=2, seqResName=LYS, pdbId=1gc1, uniProtAccessionId=P01730, notObserved=false]
  SiftsResidue [pdbResNum=3, pdbResName=VAL, chainId=C, uniProtResName=V, uniProtPos=28, naturalPos=3, seqResName=VAL, pdbId=1gc1, uniProtAccessionId=P01730, notObserved=false]
  SiftsResidue [pdbResNum=4, pdbResName=VAL, chainId=C, uniProtResName=V, uniProtPos=29, naturalPos=4, seqResName=VAL, pdbId=1gc1, uniProtAccessionId=P01730, notObserved=false]
  SiftsResidue [pdbResNum=5, pdbResName=LEU, chainId=C, uniProtResName=L, uniProtPos=30, naturalPos=5, seqResName=LEU, pdbId=1gc1, uniProtAccessionId=P01730, notObserved=false]
  SiftsResidue [pdbResNum=6, pdbResName=GLY, chainId=C, uniProtResName=G, uniProtPos=31, naturalPos=6, seqResName=GLY, pdbId=1gc1, uniProtAccessionId=P01730, notObserved=false]
  SiftsResidue [pdbResNum=7, pdbResName=LYS, chainId=C, uniProtResName=K, uniProtPos=32, naturalPos=7, seqResName=LYS, pdbId=1gc1, uniProtAccessionId=P01730, notObserved=false]
  ...
 

As you can see for each residue in the Uniprot / PDB sequence the matching counterpart is provided (if there is one).

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