The F1 moiety of the mitochondrial ATP synthase is composed of five different subunits with stoichiometry alpha 3 beta 3 gamma delta epsilon and exhibits the capacity to synthesize ATP from ADP and Pi. We have previously crystallized rat liver F1 and described its structure at 9-A resolution (Amzel, L. M., McKinney, M., Narayanan, P., and Pedersen, P. L. (1982) Proc. Natl. Acad. Sci. U. S. A. 79, 5852-5856). Here we present an x-ray map of this complex enzyme at 3.6 A, which provides a much more informative description of its quaternary structure. The overall dimensions of the F1 molecule are 120 A x 120 A x 74 A. The enzyme exhibits 3-fold symmetry relating the three copies of each of the two major subunits, alpha and beta. As the alpha subunits (but not the beta subunits) contain cysteine residues, it has been possible to identify the alpha subunits by heavy atom labeling with mersalyl and to relate their positions in the F1 molecule to the beta subunits. Significantly, the alpha and beta subunits each exist as trimeric arrays which are organized in two slightly offset, interdigitated layers along the 3-fold axis. In one trimeric layer the alpha subunits are located close to the axis with homologous subunits interacting with each other; in the other trimeric layer the beta subunits are far from the axis, and they interact only with alpha subunits and not with one another. At one end of the structure, part of the interface between each alpha and beta subunit encloses a space or "pocket" that is accessible to the solvent; at the other end the interfaces between the subunits are more open and exposed. The present work represents the highest resolution map reported to date for the F1 moiety of an ATP synthase complex.