The vacuolar H+-ATPase (V-ATPase) is an ATP-driven rotary molecular motor that is a transmembrane proton pump in all eukaryotic cells. Although its activity is fundamental to many physiological processes, our understanding of the structure and mechanism of the V-ATPase is poor. Using cryo-electron microscopy of the tobacco hornworm (Manduca sexta) enzyme, we have calculated the first 3D reconstruction of the intact pump in its native state. The resolution of 16.5 A is significantly higher than that of previous cryo-electron microscopy models of either V-ATPase or the related F1F0-ATPase. A network of four stalk structures connecting the V1 catalytic domain and the V0 membrane domain is now fully resolved, demonstrating substantially greater complexity than that found in the F-ATPase. Three peripheral stator stalks connect these domains to a horizontal collar that partly encircles the region between V1 and V0. The fourth stalk is a central axle that connects to V0 but makes minimal contact with V1. Several subunit crystal structures can be fit accurately into the reconstruction. The model thus provides new insights into the organisation of key components involved in mechanical coupling between the domains and regulation of activity.