Find and annotate a molecular interface in the complex
Identify residues involved in the interface
Steps
Navigate to Entrez Structure
On the NCBI home page, click the All Databases link on the black bar at the top.
Click on the word Structure, then click on Preview/Index.
Find structures using an Entrez query
Find all structures containing bound arginine from the genus Saccharomyces using the [ligname] and [organism] fields:
arginine[ligname] AND saccharomyces[organism]
Type this in the search box and click Preview to see how many structures match the query.
Refine the Entrez query
Now add the following to the query to limit to those structures containing one RNA chain:
AND 1[rnachaincount]
Click Preview, and then click on number of returned structures.
View the structure in Cn3D
Click the accession to open the structure summary page for this record.
Click the structure image to launch Cn3D.
Locate the molecular interface
In the sequence window, select Mouse Mode / Select Rows.
Select the entire RNA (chain B) by clicking anywhere in the sequence.
In the structure window, choose Show/Hide / Search by distance, residues only and use a radius of 3.5 Angstroms.
Display the molecular interface
Choose Show/Hide / Show Selected Residues.
Choose Style / Edit Global Style, and uncheck the boxes next to Helix Objects and Strand Objects. Click Done.
Display the protein side chains
Click anywhere in white space in the sequence window to remove the highlighting.
Choose Style / Edit Global Style, and check the box next to protein side chains, render them as ball and stick models with a color of your choice.
Display the nucleotide side chains
Check the box next to nucleotide side chains, and also render as ball and stick.
Render the nucleotide backbone as "Tubes", then choose Complete from the menu.
Click Done.
Explore charges at the molecular interface
Choose Style / Edit Global Style, and render the protein side chains as space filling models colored by charge.
What charges are present at the interface?
Explore the quality of the structural data at the molecular interface
Choose Style / Coloring Shortcuts / Temperature.
What areas of the protein and RNA are the least well determined (more red)? The most well determined (more blue)? Where are these portions relative to the interface?
Label residues in the interface
Choose Style / Global Style, and render the protein side chains as ball and stick models.
Click on the Labels tab and change the protein backbone spacing to 1. Click Done.
Examine contacts in the interface
Choose Style / Coloring Shortcuts / Molecule.
Zoom in and double click a labeled residue.
Use Show/Hide / Search by distance, Other Molecules to find RNA atoms within 3.5 Angstroms of this residue. Repeat for other residues as you like.
Draw conclusions about contacts in the interface
What are the most common amino acids involved in the contacts?
What part of the RNA is involved in most of the contacts?
