We present a mesoscopic model for ATP synthesis by F 1 F o ATPase. The model combines the existing experimental knowledge of the F 1 enzyme into a consistent mathematical model that illuminates how the stages in synthesis are related to the protein structure. For example, the model illuminates how specific interactions between the γ, ε, and α 3 β 3 subunits couple the F o motor to events at the catalytic sites. The model also elucidates the origin of ADP inhibition of F 1 in its hydrolysis mode. The methodology we develop for constructing the structure-based model should prove useful in modeling other protein motors.