The pyruvate dehydrogenase complex of Escherichia coli and subcomplexes derived from it by selective removal of component enzymes have been subjected to quaternary structural analysis by scanning transmission electron microscopy. Scanning transmission electron microscopic images of the intact complex (E1E2E3), the dihydrolipoyl transacetylase-dihydrolipoyl dehydrogenase (E2E3) subcomplex, and the E2 core enzyme appear as cubic particles in various orientations. Mass distributions within this complex and its subcomplexes have been determined by radial mass analysis of similarly oriented scanning transmission electron microscopic images of each type. The data show that mass attributable to dihydrolipoyl dehydrogenase (E3) is well integrated into the structural framework of the E2 core, dihydrolipoyl transacetylase, whereas mass attributable to pyruvate dehydrogenase (E1) is located about the periphery of the core enzyme. The mass distributions are fully consistent with a structural model in which 6 E3 dimers are integrated into the six faces of the cubic E2 core, and 12 E1 dimers are associated along the 12 edges of the core enzyme.