The three-dimensional structures of biomolecules provide a wealth of information on their biological function and evolutionary relationships. Even if a 3D structure for your protein of interest has not yet been resolved, it is possible to align your query protein to a similar sequence from a 3D structure, then interactively view the sequence/structure relationships, as shown in the illustration. Use method 1 if the protein of interest already has a sequence record in the Entrez Protein database, and use method 2 if the protein sequence is not yet in that database.

Method 1: If your protein of interest already has a sequence record in the Entrez Protein database:

1. Open the Entrez Protein search page



2. Retrieve your sequence record of interest, for example, human prostaglandin-endoperoxide synthase 1 isoform 1 precursor (accession NP_000953.2, gi 18104967), which is a product of the human PTGS1 gene (GeneID 5742).



3. Open the Links menu in the upper right corner of the protein sequence record and select Related Structure. This will retrieve a list of protein sequences that are present in 3D structure records and that were found by CBLAST to be similar to your query sequence.



4. A low redundancy list of hits is shown by default. If desired, change the View menu option to All Similar MMDB in order to see the complete list of hits. Click on the thumbnail image of any structure to read more about it. (The 1PTH structure shown in the illustration is on the third page of hits for gi 18104967; see additional notes, below.)



5. To view a sequence alignment of the query and a hit of interest, click on the pink bar that represents the alignment footprint in the graphic display of hits, or on the "view alignment" link in the last column of the table display.



6. On the sequence alignment display, press the View Structure and Alignment in Cn3D button to open an interactive view of the sequence alignment and corresponding 3D structure. The Cn3D program must be present on your computer in order for the button to work; the program is free and takes only a few minutes to install.



7. Once the Cn3D display is open, you can click on any amino acids from the retrieved structure, in either the 3D structure or the sequence alignment window, to highlight their location in both views and examine the sequence/structure relationship. The Cn3D Tutorial provides more information about using the program.

Method 2: If your sequence of interest is not yet available in the public database:

1. If you have a protein query sequence, open the Protein BLAST (blastp) page and Choose Search Set: Protein Data Bank proteins (pdb).
   
   If you have a nucleotide query sequence and want to compare its translation against protein sequences from resolved 3D structures, open the Translated BLAST (blastx) page and Choose Search Set: Protein Data Bank proteins (pdb)



2. Enter your query sequence in FASTA format. If desired, adjust the algorithm parameters to make the search more or less stringent than the default, then press the blue BLAST button at the bottom of the query page to execute the search.



3. Once the BLAST search results appear, scroll down to the Descriptions portion of the results and press the red "S" button beside any hit of interest to view that hit aligned to your query sequence on the CBLAST display. From there, you can follow steps 5+ in Method 1, above, to open an interactive view of the query sequence and the structure in Cn3D.

Additional Notes:

1. A query protein sequence can potentially retrieve many similar 3D-structure-based sequences. Some of the structures might be free proteins, other might be bound to another molecule such as a chemical or other protein. The salient features of each structure are described in the publication(s) cited on its MMDB summary page, accessible by clicking on a structure's thumbnail image.



2. The 1PTH structure shown in the illustration is on the third page of hits for gi 18104967, as of 22 June 2009. It is featured here because it shows a chemical, salicylic acid, blocking the channel that leads to the protein's active site. Though it is a ovine protein, it is homologous to the human protein and can therefore be helpful in elucidating the biological function of the human protein.



3. The specific view shown in the illustration was generated by following steps 1-6 of method 1, then: (a) zooming into protein's active site region in the 3D structure window; (b) double-clicking on the salicylic acid to highlight it; (c) selecting Show/Hide -> Select by distance -> Residues Only -> 5 Angstroms to reveal the amino acids that are within that distance of the highlighted chemical, and (d) panning across the sequence data to see which amino acids were highlighted in the sequence data.

See Also:      How to find structures for a gene/protein product of interest.