F₁ ATPase

PDB file 1BMF

This structure of bovine mitochondrial F₁ ATPase with bound nucleotides was solved by J. P. Abrahams, A. G. W. Leslie, R. Lutter, & J. E. Walker in 1996.

Suggested display options:

Protein: Display as ribbons and color chain to give each subunit a different color.
Rotate to view the complex looking at the ring of a & b subunits, along the axis of the g subunit helixes, and then with the g subunit "shaft" parallel to the screen.
Note how the bent helical loop of g extends up into the ring of a & b subunits.
Also view with the protein in spacefill display.

Ligands: Position the complex end on, with the g tail pointing out from the screen.
To make the protein disappear, select protein and then hide selected.
Select ligand, display as ball & stick, or spacefill, and color CPK.
For orientation and to visualize the g subunit, select *g and display as spacefill.

Identify the three catalytic b subunits by their variation in bound nucleotides.

• One b has bound AMPPNP, a non-hydrolyzable ATP analog (look for the extra N).
• One b has bound ADP.
• The third b has an empty active site.

Questions:

• What nucleotide is bound to each a subunit?
• Where are Mg⁺⁺ ions located relative to the nucleotides? 
• What is the shape of the g subunit? How is this relevant?

With the nucleotides visible, bring back the rest of the protein by selecting protein, and display as wireframe.

Crystallographic data are consistent with a role of an a-subunit arginine side-chain in adjusting the position of the substrate/product water molecule at each b-subunit active site depending on the presence or absence of the terminal phosphate of ATP.
Question: Is the location of each active site within the b-subunit consistent with such a role of the adjacent a subunit?

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