Two-dimensional crystals of rhodopsin were studied to determine the arrangement of the transmembrane alpha helices. A combination of electron cryomicroscopy, image processing and electron crystallography was used to extract amplitudes and phases from images, and a three-dimensional map to a resolution of 7.5 A was calculated. Density peaks for all seven transmembrane helices were observed and the helix axes for all seven helices could be estimated. Near the intracellular side, which interacts with the G protein transducin, we observed three layers of helices arranged differently from bacteriorhodopsin. The arrangement opens up towards the extracellular side forming a cavity that serves as the binding pocket for the retinal. This cavity is closed towards the intracellular side by the long and highly tilted helix 3, and must be closed towards the extracellular side by the loop linking helices 4 and 5 which is linked by a disulfide bridge to the extracellular end of helix 3.