Colouring a Protein Complex to Explore Domain-Domain Interfaces

  1. Download the PDB file at to your desktop. This is the biological unit for PDB ID 3pt6, as identified by the PDBe’s PISA server.

  2. Retrieve the following PFAM alignments PF02008, PF01426 and PF00145 separately from the PFAM (full) source into their own alignment window.

  3. Drag the URL or file of the structure you downloaded in step 1 onto one of the alignments to associate it with the mouse sequence in that Pfam domain family.

  4. Locate every DNMT1_MOUSE sequence in the alignment by opening the Select $\Rightarrow$ Find dialog box and search using the text DNMT1_MOUSE. (If the sequence isn’t found, use [ESC] key to deselect resides). Right click the mouse on sequence name to open the context menu, and selecting $\Rightarrow$ 3D Structure Data. In the Structure Chooser dialog box, select ‘Cached Structures’ from the drop-down menu and select the DNMT1_MOUSE structure from the list, then click Open new structure view with Jmol. Part of the newly opened structure will be coloured as the associated DNMT1_MOUSE sequence is in the alignment view.

WARNING: do not select all sequences and open the Structure Chooser. As this will cause Jalview to attempt to discover all structures for sequences in the alignment.

  1. Repeat the previous steps for the other two alignments but select Add to ensure each domain alignment is associated with the same Jmol view. Also ensure the Superpose Structures box is ticked in the Structure Chooser dialog box.

Note: If the structure is coloured green, disable the View $\Rightarrow$ Show Sequence Features menu option.

  1. Finally Colour $\Rightarrow$ By Annotation. . . option in each alignment window to shade the alignment by the Conservation annotation row. In the Colour by Annotation dialog box, select Conservation and No Threshold in the drop-down menu, then select different colours for each sequence. Examine the regions strongly coloured at the interfaces between each protein domain, and the DNA binding region. What do you think these patterns mean?
For more information on this topic go to chapter.7 of the Jalview manual.