The re-entry of protons into the mitochondrial matrix through Complex V causes conformational changes which result in ATP synthesis. Complex V (ATP synthase) is composed of 3 parts; an F1 catalytic core (approx 5 subunits), an F0 membrane proton channel (approx 9 subunits) and two stalks linking F1 to F0. F1 contains three alpha subunits, three beta subunits, and one each of gamma, delta, and epsilon subunits. Each beta subunit contains an active site for ATP synthesis. F0 has at least 9 subunits (a-g, A6L and F6), with one copy each of subunits b, d and F6.
The mechanism of ATP synthesis by Complex V was predicted by Boyer et al in 1973: ADP and Pi bind to the enzyme resulting in a conformational change. ATP is then synthesized, still bound to the enzyme. Another change in the active site results in the release of free ATP into the matrix. The overall reaction is:
ADP + Pi + H+ + nH+ (intermemb. space) = ATP + H2O + nH+ (matrix)