The ATPase (ATP synthase) complex of Escherichia coli is composed of an extrinsic membrane protein (ECF1), which contains the active site for ATP formation and hydrolysis, and is attached to ECF0, a transmembrane protein through which protons move to or from the active site on ECF1. ECF1 is composed of five subunits (α–ε) with a stoichiometry of α3β3γδε. The stoichiometry of the three subunits (a–c) of ECF0 is probably a1b2c10–15. In addition to 3 mol tightly bound adenine nucleotide/mol ECF1, three other "exchangeable" nucleotide binding sites can be detected. These sites are still present in the α and β subunit defective ECF1 of uncA401 and uncD412 mutants, although some changes in the tightness of binding are evident. The active sites of ECF1 require normal a and p subunits and may be present at αβ subunit interfaces. Hydrolysis of ATP requires cooperative interactions between α and β subunits. At low concentrations of ATP, in the absence of added divalent cations, hydrolysis of this substrate can occur at a single site without release of the product. This is consistent with alternating or sequential site mechanisms for ATP hydrolysis or synthesis. Predictions of secondary and tertiary structures from the known primary amino acid sequences of polypeptides a, b, and c have led to the following conclusions. Polypeptide a forms six or seven transmembrane a helices. The amino-terminal sequence of polypeptide b spans the membrane, but most of the protein is exposed on the cytoplasmic surface of the membrane where it can be cleaved by proteases in vitro. Polypeptide c consists of two nonpolar membrane-spanning α helices linked by a polar segment at the cytoplasmic surface of the membrane. This loop region interacts with ECF1 or is close to the ECF1-binding site. This is shown by competition between ECF1 and antibody for binding to polypeptide c. Chemical modification of arginyl residues in the loop region of polypeptide c inhibits ECF1 binding. Protease cleavage of polypeptide b affects, but does not abolish, binding of ECF1 to ECF0. Presumably, polypeptide b interacts with ECF1 also. The individual roles of the ECF0 polypeptides in proton translocation are not clear. Mutants in any of the three polypeptides may be defective in proton translocation. However, mutant and chemical modification studies support a role for the polypeptide c oligomer in the transmembrane proton pathway.