Structure of yeast RAVE bound to a partial V₁ complex

Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multisubunit enzymes consist of a soluble catalytic V₁ subcomplex and a membrane-embedded proton-translocating V_O subcomplex. The V₁ and V_O subcomplexes can undergo reversible dissociation to regulate proton pumping, with reassociation of V₁ and V_O requiring the protein complex known as RAVE (regulator of the ATPase of vacuoles and endosomes). In the yeast Saccharomyces cerevisiae, RAVE consists of subunits Rav1p, Rav2p, and Skp1p. We used electron cryomicroscopy (cryo-EM) to determine a structure of yeast RAVE bound to V₁. In the structure, RAVE is an L-shaped complex with Rav2p pointing toward the membrane and Skp1p distant from both the membrane and V₁. Only Rav1p interacts with V₁, binding to a region of subunit A not found in the corresponding ATP synthase subunit. When bound to RAVE, V₁ is in a rotational state suitable for binding the free V_O complex, but in the structure, it is partially disrupted, missing five of its 16 subunits. Other than these missing subunits and the conformation of the inhibitory subunit H, the V₁ complex with RAVE appears poised for reassembly with V_O.