ClpAP, an ATP-dependent protease of E. coli, recognizes and unfolds protein substrates via ClpA, its chaperonelike ATPase component, and digests them in ClpP, its protease component . ClpA forms hexameric rings with a two-layered structure, and stacks axially on either face of the double heptameric rings of ClpP. Protein substrates can bind to ClpAP in the presence of ATPγS, which is not hydrolyzed by ClpA, but are not degraded unless ATP is added. This property makes it possible to synchronize degradation in vitro by forming enzymesubstrate complexes in the presence of ATPγS and then adding ATP to trigger subsequent steps. We have used image averaging of electron micrographs of frozen hydrated and negatively stained specimens to characterize interactions of ClpA and ClpAP complexes with the model substrate, bacteriophage P1 protein, RepA.