Aligning Structures using the Ferredoxin Sequence Alignment

1. Continue with the Jalview project created in previous exercise.

2. Select the FER1_MAIZE sequence (near bottom of the alignment). Right-click the ID label to open the context menu, select $\Rightarrow$ 3D Structure Data.

3. This opens the Structure Chooser dialog, pick 1gaq or 3b2f from the list. Make sure the Superpose option is checked before clicking the Add button. This superimpose the structure associated with FER1_MAIZE with the one associated with FER1_SPIOL. Note: The Jmol view should update to show both structures, and one will be moved on to the other. If this doesn’t happen, use the Align function in the Jmol submenu.

4. Create a new view on the alignment (View $\Rightarrow$ New View), and hide all but columns 121 through to 132 (View $\Rightarrow$ Hide $\Rightarrow$ All but selected region).

5. Select the newly created view in the structure window using Jmol $\Rightarrow$ Superpose With submenu, and then recompute the superposition with Jmol $\Rightarrow$ Superpose Structures.

   Note: how the molecules shift position when superposed with only a small region of the alignment.

6. Compare RMSDs obtained when superimposing molecules with columns 121-132 and with the whole alignment. The RMSD report can be viewed by right clicking the mouse on Jmol window, and select Console from the menu (if nothing is shown, re- compute the superposition after displaying the console).

7. Which view do you think give the best 3D superposition, and why?