Structural basis of V-ATPase V(O) region assembly by Vma12p, 21p, and 22p

Vacuolar-type adenosine triphosphatases (V-ATPases) are rotary proton pumps that acidify specific intracellular compartments in almost all eukaryotic cells. These multi-subunit enzymes consist of a soluble catalytic V(1) region and a membrane-embedded proton-translocating V(O) region. V(O) is assembled in the endoplasmic reticulum (ER) membrane, and V(1) is assembled in the cytosol. However, V(1) binds V(O) only after V(O) is transported to the Golgi membrane, thereby preventing acidification of the ER. We isolated V(O) complexes and subcomplexes from Saccharomyces cerevisiae bound to V-ATPase assembly factors Vma12p, Vma21p, and Vma22p. Electron cryomicroscopy shows how the Vma12-22p complex recruits subunits a, e, and f to the rotor ring of V(O) while blocking premature binding of V(1). Vma21p, which contains an ER-retrieval motif, binds the V(O):Vma12-22p complex, “mature” V(O), and a complex that appears to contain a ring of loosely packed rotor subunits and the proteins YAR027W and YAR028W. The structures suggest that Vma21p binds assembly intermediates that contain a rotor ring and that activation of proton pumping following assembly of V(1) with V(O) removes Vma21p, allowing V-ATPase to remain in the Golgi. Together, these structures show how Vma12-22p and Vma21p function in V-ATPase assembly and quality control, ensuring the enzyme acidifies only its intended cellular targets.