Use BLink to find a structure corresponding to a protein sequence
Locate the position of a SNP in the structure using Cn3D
Create an annotation of the region near the SNP
Steps
Retrieve the protein sequence for human HFE
On the NCBI home page, enter NP_000401 in the search box and click Go.
Click on the number of protein hits.
What is this protein?
Find a sequence-similar structure
Click on "Related Structure" in the Links menu to the right of the accession.
Change the List menu from 'All MMDB' to 'Non-identical' and click List.
What is the most sequence-similar structure (the one with the lowest e-value)? Is it a full or partial sequence match?
View the related structure in Cn3D
Click on the red bar representing the most sequence-similar structure (to the right of its
accession).
On the Related Structures page, click 'Get 3D Structure data'.
Cn3D should launch. Compare the two sequences (red = identical residues, blue = non-identical residues).
Locate a SNP in Cn3D
Find C282 in NP_000401 (a position of a known SNP) by pointing your mouse over the residues in the second sequence. The residue numbers will be shown in the lower left of the sequence window.
In the sequence window, click on the residue in the structure aligned to C282 (the top sequence).
Find the residue in the structure. In what structural feature is the residue involved?
Annotate the region near the SNP
In the structure window, double click the residue connected to the residue that you highlighted in the previous step. What residue is this?
Choose Style / Annotate, click "New", and give the annotation a name.
Click Edit Style, and check the box next to protein side chains. Render them as ball and sticks, and color them as you choose.
Label the residues near the SNP
Click the Labels tab and change the spacing to 1 under protein backbone. If labels don't appear, click Apply.
Click Done, OK, and Done.
If the virtual bond between the residues is still visible, select Style / Edit Global Style and uncheck "Virtual Disulfides".
Interpret your results
What structural role does the residue play that aligns to C282 in NP_000401?
What could be the consequence of mutating this residue to a tyrosine?
