Deregulation of the ubiquitin ligase E6AP is causally linked to the development of human disease, including cervical cancer. In complex with the E6 oncoprotein of human papillomaviruses, E6AP targets the tumor suppressor p53 for degradation, thereby contributing to carcinogenesis. Moreover, E6 acts as a potent activator of E6AP by a yet unknown mechanism. However, structural information explaining how the E6AP-E6-p53 enzyme-substrate complex is assembled, and how E6 stimulates E6AP, is largely missing. We therefore developed and applied different approaches in structural mass spectrometry to show that binding of E6 induces conformational rearrangements in E6AP, which result in the positioning of E6 and p53 in the immediate vicinity of the catalytic centre of E6AP. Our data provides structural and functional insights into the dynamics of the full-length E6AP-E6-p53 enzyme-substrate complex and reveals how E6 can both stimulate the ubiquitin ligase activity of E6AP and facilitate the transfer of ubiquitin from E6AP onto p53.