H(+)-ATPase is a P-type ATPase that transports protons across membranes using the energy from ATP hydrolysis. This hydrolysis is coupled to a conformational change between states of the protein, in which the proton-binding site is alternately accessible to the two sides of the membrane with an altered affinity. When isolated from Neurospora crassa, H(+)-ATPase is a 600 kDa hexamer of identical 100 kDa polypeptides. We have obtained the three-dimensional structures of both ligand-free and Mg(2+)/ADP-bound states of this complex using single-particle electron cryo- microscopy. Structural comparisons, together with the difference map, indicate that there is a rearrangement of the cytoplasmic domain on Mg(2+)/ADP binding, which consists of a movement of mass towards the 6-fold axis causing the structure to become more compact, accompanied by a modest conformational change in the transmembrane domain.