In Archaea, bacteria, and eukarya, ATP provides metabolic energy for energy-dependent processes. It is synthesized by enzymes known as A-type or F-type ATP synthase, which are the smallest rotatory engines in mature (Yoshida, M., Muneyuki, E., and Hisabori, T. (2001) Nat Rev. Mol. Cell Biol. 2, 689-677; Imamura, H., Nakano, M., Noji, H., Muneyuki, E., Ohkuma, S., Yoshida, M., and Yokoyama, E. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 2312-2315). Here, we report the first projected structure of an intact A₁A₀ ATP synthase from Methanococcus jannaschii as determined by electron microscopy and single particle analysis at a resolution of 1.8 nm. The enzyme with an overall length of 25.9 nm is organized in an A₁ headpiece (9.4 x 11.5 nm) and a membrane domain, A₀ (6.4 x 10.6 nm), which are linked by a central stalk with a length of ∼8 nm. A part of the central stalk is surrounded by a horizontal-situated rod-like structure ("collar"), which interacts with a peripheral stalk extending from the A₀ domain up to the top of the A₁ portion, and a second structure connecting the collar structure with A₁. Superposition of the three-dimensional reconstruction and the solution structure of the A₁ complex from Methanosarcina mazei Gö1 have allowed the projections to be interpreted as the A₁ headpiece, a central and the peripheral stalk, and the integral A₀ domain. Finally, the structural organization of the A₁A₀ complex is discussed in tenus of the structural relationship to the related motors, F₁F₀ ATP synthase and V₁V₀ ATPases.