Open the protein sequence P00656 by clicking here. Turn on the annotations if necessary and you will see that there are many structural features identified. Make sure you have the Alpha Helix, Beta Strand, Bond, Region and Site annotations checked.
Note that there are secondary structures indicated using type specific cartoons. This protein has a mixture of α-helices, β-strands and turns. These secondary structure annotations have been derived from crystal structures of this protein. Look at the Text View for this sequence and you will see references to a number of publications. To find the crystal structures that this sequence correspond to you should click the View GenBank record on NCBI website as this provides database cross-references. Under DBSOURCE you will see a list of four character PDB names including 5RSA which you have been using already.
Before returning to the three-dimensional PDB structure, you need to edit the protein sequence you are currently viewing (P00656). This is because there is additional sequence which is not present in the crystal data and it will be easier to trace features in the structure if the sequences are identical. Notice that residues 1-26 of P00656 are annotated as Signal.
To remove this, click the Allow Editing button on the sequence viewer tool bar. Now click on the Signal annotation and press the Delete key and choose to remove both the annotation and the sequence itself. Finally, click
Save to preserve your change.
Each time you click Find Next Geneious will jump to the next annotation that mentions active. At the bottom of the sequence viewer it will tell you which residue is selected. Note each one and you should find they are 12, 41 and 119. These three residues form a catalytic triad that bind divalent cations. Since they are widely spaced in the linear sequence, it will be interesting to highlight their position in the 3D structure to see their actual proximity.
First you need to make the majority of the structure a simple background for the highlighted residues to appear against. Make sure you have selected the whole structure using Select and clicking All. The Cartoon style looks attractive and should suit. Also, color the structure by the Structure scheme. Now you can see the helices, sheets and turns. Next, select residues 12, 41 and 119 in the selection tree by expanding chain A out and selecting each while holding the CTRL (Windows/Linux) or Command (Mac) keys. When you have selected these three residues, select the Sticks style. This will only affect the selected residues. Finally, color them using plain colors. Cyan stands out well so use that.
You should now see where these three active site residues are and note that they are all directed towards the centre of the RNA binding cleft. More information on Ribonuclease A can be found at: http://en.wikipedia.org/wiki/Ribonuclease_A
When you have finished setting up your molecule, you can click the Save button and the state will be preserved for the next time you open the document.
Congratulations, you have completed this tutorial.