Mitochondrial ATP synthase: Quaternary structure of the F₁ moiety at 3.6 Å determined by x-ray diffraction analysis

The F₁ moiety of the mitochondrial ATP synthase is composed of five different subunits with stoichiometry α₃β₃γδε and exhibits the capacity to synthesize ATP from ADP and P_i. We have previously crystallized rat liver F₁ and described its structure at 9-Å 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 Å, which provides a much more informative description of its quaternary structure. The overall dimensions of the F₁ molecule are 120 Å × 120 Å × 74 Å. The enzyme exhibits 3-fold symmetry relating the three copies of each of the two major subunits, α and β. As the α subunits (but not the β subunits) contain cysteine residues, it has been possible to identify the α subunits by heavy atom labeling with mersalyl and to relate their positions in the F₁ molecule to the β subunits. Significantly, the α and β 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 α subunits are located close to the axis with homologous subunits interacting with each other; in the other trimeric layer the β subunits are far from the axis, and they interact only with α subunits and not with one another. At one end of the structure, part of the interface between each α and β 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.