Structure of the vacuolar ATPase by electron microscopy

The structure of the vacuolar ATPase from bovine brain clathrin-coated vesicles has been determined by electron microscopy of negatively stained, detergent-solubilized enzyme molecules. Preparations of both lipid-containing and delipidated enzyme have been analyzed, The complex is organized in two major domains, a V-1 and V-0, with overall dimensions of 28 x 14 x 14 nm, The V-1 is a more or less spherical molecule with a central cavity. The V-0 has the shape of a flattened sphere or doughnut with a radius of about 100 Angstrom. The V-1 and V-0 are joined by a 60-Angstrom long and 40-Angstrom wide central stalk, consisting of several individual protein densities. Two kinds of smaller densities are visible at the top periphery of the V-1, and one of these seems to extend all the way down to the stalk domain in some averages. Images of both the lipid-containing and the delipidated complex show a 30-50-kDa protein density on the lumenal side of the complex, opposite the central stalk, centered in the ring of c subunits. A large trans-membrane mass, probably the C-terminal domain of the 100-kDa subunit a, is seen at the periphery of the c subunit ring in some projections. This large mass has both a lumenal and a cytosolic domain, and it is the cytosolic domain that interacts with the central stalk. Two to three additional protein densities can be seen in the V-1-V-0 interface, all connected to the central stalk. Overall, the structure of the V-ATPase is similar to the structure of the related F1F0-ATP synthase, confirming their common origin.