The structure of the vacuolar ATPase from bovine brain clathrin-coated vesi
cles has been determined by electron microscopy of negatively stained, dete
rgent-solubilized enzyme molecules. Preparations of both lipid-containing a
nd delipidated enzyme have been analyzed, The complex is organized in two m
ajor domains, a V-1 and V-0, with overall dimensions of 28 x 14 x 14 nm, Th
e V-1 is a more or less spherical molecule with a central cavity. The V-0 h
as the shape of a flattened sphere or doughnut with a radius of about 100 A
ngstrom. The V-1 and V-0 are joined by a 60-Angstrom long and 40-Angstrom w
ide 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 s
how a 30-50-kDa protein density on the lumenal side of the complex, opposit
e the central stalk, centered in the ring of c subunits. A large trans-memb
rane 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 mas
s 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 den
sities can be seen in the V-1-V-0 interface, all connected to the central s
talk. Overall, the structure of the V-ATPase is similar to the structure of
the related F1F0-ATP synthase, confirming their common origin.