F-ATP synthases are the most prominent source of ATP in living cells. Residing in the membranes of bacteria and mitochondria, these enzymes catalyze the conversion of ADP and Pi into ATP, through a structural mechanism that is coupled to the transmembrane flow of protons or sodium ions down their electrochemical gradients. The key coupling element in these molecular machines is a membrane-embedded tubine-like structure, or c-ring. The increased availability of structural data and the close interplay of experimental methods with molecular simulations are providing novel and important insights into the mechanisms of these essential enzymes. I will present an overall summary of our recent progress in this area, particularly pertaining to the structural basis for the distinct ion-binding selectivity observed in different species, and to the mechanism by which ions are loaded and released from the c-ring at it rotates within the membrane. To conclude, I will describe recent investigations into the self-organization of ATP synthases in mitochondrial membranes, and speculate about its implications on the membrane morphology.