On the basis of x-ray diffraction data to a resolution of 2.9 angstroms, atomic models of most protein components of the bovine cytochrome bc(1) complex were built, including core 1, core 2, cytochrome b, subunit 6 subunit 7, a carboxyl-terminal fragment of cytochrome c(1), and an amino-terminal fragment of the iron-sulfur protein. The positions of the four iron centers within the be, complex and the binding sites of the two specific respiratory inhibitors antimycin A and myxothiazol were identified. The membrane-spanning region of each bc(1) complex monomer consists of 13 transmembrane helices, eight of which belong to cytochrome b. Closely interacting monomers are arranged as symmetric dimers and form cavities through which the inhibitor binding pockets can be accessed. The proteins core 1 and core 2 are structurally similar to each other and consist of two domains of roughly equal size and identical folding topology.