PDB/UniProt Info

PDB/UniProt Info retrieves annotations for Protein Data Bank (PDB) entries using a web service provided by the RCSB PDB. Sequences are displayed in Multalign Viewer, and feature annotations from UniProt are mapped onto the sequences as regions. See also: fetching UniProt data

There are several ways to start PDB/UniProt Info, a tool in the Sequence category. It is also available as the UniProt info... function in the Model Panel.

The top part of the initial dialog lists the PDB chains currently open in Chimera. One or more chains can be chosen with the left mouse button. Choosing a chain uses its PDB ID to retrieve structure annotations and any PDB-UniProt mapping information (UniProt ID and residue number correspondences) from the RCSB PDB. The information is fetched as an XML file that can be cached and reused as needed depending on the Fetch preferences and whether the option to Ignore any cached data is checked. A dialog will appear for entering the PDB ID if it cannot be determined automatically. If the chain does not correspond to an entry in the PDB, no information can be retrieved. Sequence annotations are fetched from UniProt; these are not cached.

• Structure annotations. For valid PDB entries, the bottom part of the initial dialog will also show entry title, primary literature citation, structure determination method, source organism, and release date annotations from the RCSB PDB. One or more entries can be chosen in the bottom part of the dialog. Clicking Show PubMed page will display (in a browser window) the primary citation abstract at PubMed for each chosen entry.
  
  
• Sequence annotations. Additional windows will appear for showing sequence feature annotations from UniProt, if available. Not all PDB chains are annotated with a UniProt ID, and a given PDB entry may contain both chains with and without UniProt IDs. For each chain with a UniProt ID:
  
  
  • the amino acid sequence from UniProt will be displayed in the Sequence tool (also known as Multalign Viewer), numbered according to the structure
    
    
  • the UniProt sequence features will be listed as regions in the Multalign Viewer Region Browser; this dialog controls the display of regions in the sequence window. Full details are in the Region Browser documentation, but briefly:
    
    
    • any parts of the sequence not present in the structure will be shown as a pinkish outline region named missing structure...
      
      
    • making a region Active selects the corresponding structure residues for subsequent operations with the Actions menu (in the example, the LDL receptor binding region was selected, its atoms/bonds were shown, it was colored cyan and then by heteroatom, and then the selection was cleared)
      
      
    • making a region Shown displays it in the sequence window
      
      
    • region colors can be changed by clicking the square color wells and using the Color Editor; one column of wells is for interior colors, the other for outline colors
    
    
  • clicking Show UniProt page(s) will display the corresponding web page(s) at UniProt (example)