How to: View a mutation site in a 3D structure

Starting with...

A SNP RS NUMBER (E.G. rs58524323)

  1. Search for the rs number in Entrez SNP.
  2. Click on the Protein 3D box in the graphic summary.
  3. In the resulting table, three amino acids are listed for each SNP: the residue in the reference protein (e.g., NP_000231; protein context), the residue change due to the SNP, and the residue in the most sequence-similar structure (structure neighbor). Check the boxes under "Cn3D" for each SNP of interest. Click the "Selected" button.
  4. On the next page, the SNPs are shown as colored triangles on the grey bar representing the protein sequence. Matching structures are listed below. Click on a pink bar representing a structure.
  5. To view the alignment in Cn3D with the SNP positions highlighted, click the "View structure and alignment in Cn3D" button.

THE POSITION OF THE SNP IN A PDB SEQUENCE

  1. Go to the Structure Home Page.
  2. Enter the PDB code in the search box and press the Go button.
  3. Click the structure image, and on the resulting page click the "Structure View in Cn3D" button.
  4. In the Sequence/Alignment window of Cn3D, find the SNP position by pointing your mouse at residues in the sequence and reading the position number in the lower left corner of the window.
  5. Click the residue at the SNP position, which should now turn yellow in the sequence and in the structure view. For more information, please see the Cn3D tutorial.

THE POSITION OF THE SNP IN A PROTEIN WITH AN ACCESSION NUMBER (e.g. NP_000231)

  1. Go to the Protein Home Page.
  2. Enter the protein accession number in the search box and press the Go button.
  3. Click on the Links pulldown in the upper right and select "Related Structures".
  4. The similar structures will be shown as pink bars below the query sequence. Using the coordinate axis, select a structure that contains the SNP position. Click on the pink bar.
  5. To view the alignment in Cn3D with the SNP positions highlighted, click the "View structure and alignment in Cn3D" button.

THE POSITION OF THE SNP IN A PROTEIN SEQUENCE

  1. Go to the BLAST home page.
  2. Click on "protein blast" under Basic BLAST.
  3. Paste the protein sequence in the query box and change the Database pulldown menu to "Protein Data Bank proteins (PDB)". Click the BLAST button.
  4. When the search is finished, click the "Related Structures" link near the top of the report.
  5. Continue with step 4 under "the position of the SNP in a protein with an accession number" above.
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