The vacuolar (H ؉ )-ATPases (or V-ATPases) are structurally related to the F 1 F 0 ATP synthases of mitochondria, chloroplasts and bacteria, being composed of a peripheral (V 1 ) and an integral (V 0 ) domain. To further investigate the arrangement of subunits in the V-ATPase complex, covalent cross-linking has been carried out on the V-ATPase from clathrin-coated vesicles using three different cross-linking reagents. Crosslinked products were identified by molecular weight and by Western blot analysis using polyclonal antibodies raised against individual V-ATPase subunits. In the intact V 1 V 0 complex, evidence for cross-linking of subunits C and E, D and F, as well as E and G by disuccinimidyl glutarate was obtained, while in the free V 1 domain, cross-linking of subunits H and E was also observed. Subunits C and E as well as D and E could be cross-linked by 1-ethyl-3-(dimethylaminopropyl)carbodiimide, while subunits a and E could be cross-linked by 4-(N-maleimido)benzophenone. It was further demonstrated that it is possible to treat the V-ATPase with potassium iodide and MgATP in such a way that while subunits A, B, and H are nearly quantitatively removed, significant amounts of subunits C, D, E, and F remain attached to the membrane, suggesting that one or more of these latter subunits are in contact with the V 0 domain. In addition, treatment of the V-ATPase with cystine, which modifies Cys-254 of the catalytic A subunit, results in dissociation of subunit H, suggesting communication between the catalytic nucleotide binding site and subunit H. Finally, the stoichiometry of subunits F, G, and H were determined by quantitative amino acid analysis. Based on these and previous observations, a new structural model of the V-ATPase from clathrincoated vesicles is proposed.The vacuolar (H ϩ )-ATPases (or V-ATPases) 1 are a family of ATP-dependent proton pumps that carry out proton transport across both intracellular membranes and, in some cases, the plasma membrane (1-6). Acidification of intracellular compartments is important for such processes as protein degradation, intracellular protein targeting, and receptor-mediated endocytosis (1-6), while V-ATPases in the plasma membrane function in renal acidification, bone resorption, and tumor metastasis (7-9).The V-ATPase is a heteroligomeric complex of molecular mass approximately 800 kDa composed of at least 13 different subunits arranged into two separate domains (1-6). The peripheral V 1 domain has a molecular mass of about 570 kDa and contains eight different subunits of molecular mass 70 (A), 60 (B), 57 (H), 40 (C), 34 (D), 33 (E), 14 (F), and 16 (G) kDa. The integral V 0 domain has a molecular mass of 260 kDa and contains five different subunits of molecular mass 100 (a), 38 (d), 19 (cЉ), and 17 (c, cЈ) kDa. Functional studies indicate that the V 1 domain is responsible for ATP hydrolysis while the V 0 domain carries out proton transport (1-6). We have previously demonstrated that each V-ATPase complex contains three copies each of the A and B subunits, six co...