Aligning F-ATPase alpha and beta subunits

Start SPdbV

Open 1bmf.pdb

Color Chain

Change color chainD to grey/blue (rightclick in control panel on D in first column to select chain D, right click on COL, select color)

Scrol down the control panel and select all ATP analogs (press ctrl key and right click to select)

right click on COL in heading and select red color

Read the pdb file to get info on which chain is which

select chain F (including nuc) and save selected residues as betaTP.

select chain A (including nuc) and save selected residues as alphaE.

After playing with the F1-ATPase, close this file and open betaTP and alphaE.

Display layer info

select and display only the nucleotides

There are different ways to align 3-D structures. One way is to select 3 corresponding points in each of the two structures. To do so you can use the substrate molecule.

Using the mov check off in the Layer Info, reorient the two ANPs so that they are in a similar orientation (but not overlapping).

Click on the align bottom with the 3 green and 3 red dots. Notice the red instructions that appear in the header next to the pdb-page icon. Follow these instruction using three corresponding atoms.

SHIFT DISPLAY CA chain (Shift makes the commands act on both layers)

Using the mov checks in the Layer info, move the two chains next to each other.

What do you think about the result?

Another way to align structures is to use the magic fit in the tools command. Do this and run improve fit (notice the red info in the header)

Click on alpha in Layer info to make the alpha subunit the active layer

Color CPK

Make the beta subunit the active layer

COLOR rms . The further the atoms in the beta subunit are away from the alpha subunit, the longer wavelengths it is the colored.

DISPLAY Show alignment window - gives you the aligned sequences.

How does this alignment compare to the ones calculated using Clustalw?

If you have time, repeat the exercise for the three beta subunits to observe the structural changes the beta subunit is undergoing in the catalytic cycle.

OPTIONAL

If you have more time to spare and you are up for a challenge, take a look at the nucleosome. Right click here and save as pdb file. Open it from within spdbv. You might want to do some of the future exercises with the nucleosome in addition to the ATPases – thus save the pdb file, where you can find it again.

Align all the histones form the nucleosome to one reference histone and color in rmv:

The result might look something like this:

The picture shows a structure alignment of the 8 histones (2 each) that are part of the nucleosome. All the histones were colored regarding the match to H2A, except H2A, which was colored according to its match to H3. Coloring option RMS – shorter wavelengths – better match

 Below same as last figure, but histones are depicted side by side

Below are two views of the complete nucleosome. Histones H2A are depicted as spacefilling balls and RMS colored regarding their match to H3. The rest of the molecule is colored according to chain.