Recombinant, bacterially expressed apoptin protein induces apoptosis in human tumour cell lines but not in normal cells, mimicking the behaviour of ectopically expressed apoptin. Recombinant apoptin is isolated exclusively as a highly stable multimeric complex of 30-40 monomers, with little, if any, alpha-helical and beta-sheet structure. Despite its apparent disorder, multimeric apoptin is biologically active. Here, we present evidence that most of the apoptin moieties within the complex may well share a similar conformation. Furthermore, the multimer has extensive and uniform hydrophobic patches and conformationally stable domains. Only a small fraction of apoptin subunits can exchange between multimers under physiologically relevant conditions. These results prompt a model in which the apoptin multimer has a highly stable core of nonexchangeable subunits to which exchangeable subunits are attached through hydrophobic interactions. In combination with previous findings, our results lead us to propose that the stable core of apoptin is the biologically relevant structure.