We have begun to define the human papillomavirus (HPV)-associated proteome for a subset of the more than 120 HPV types that have been identified to date. Our approach uses a mass spectrometry-based platform for the systematic identification of interactions between human papillomavirus and host cellular proteins, and here we report a proteomic analysis of the E6 proteins from 16 different HPV types. The viruses included represent high-risk, low-risk, and non-cancer-associated types from genus alpha as well as viruses from four different species in genus beta. The E6 interaction data set consists of 153 cellular proteins, including several previously reported HPV E6 interactors such as p53, E6AP, MAML1, and p300/CBP and proteins containing PDZ domains. We report the genus-specific binding of E6s to either E6AP or MAML1, define the specific HPV E6s that bind to p300, and demonstrate several new features of interactions involving beta HPV E6s. In particular, we report that several beta HPV E6s bind to proteins containing PDZ domains and that at least two beta HPV E6s bind to p53. Finally, we report the newly discovered interaction of proteins of E6 of beta genus, species 2, with the Ccr4-Not complex, the first report of a viral protein binding to this complex. This data set represents a comprehensive survey of E6 binding partners that provides a resource for the HPV field and will allow continued studies on the diverse biology of the human papillomaviruses.T he human papillomaviruses (HPVs) comprise more than 120 different virus types, each with a double-stranded DNA genome of approximately 8 kb. The HPVs have similar genome organizations, with regulatory functions encoded by the early (E) genes and structural components encoded by the late (L) genes (reviewed in reference 24). HPVs of different types differ in DNA sequences by 10% or more in the L1 gene, and the other viral genes exhibit a greater degree of sequence diversity between types (6, 15). Papillomaviruses are grouped into genera based on their L1 gene sequences and are further subdivided into species, with most of the HPVs in genus alpha or genus beta. The genus alpha HPVs infect the mucosal epithelium, and those that are the etiological agent responsible for the development of anogenital cancers (including cervical cancer) fall into genus alpha, species 7, and genus alpha, species 9. Beta-type HPVs infect the cutaneous epithelium.The HPV E6 protein has long been appreciated as a critical regulator of the viral life cycle and driver of tumorigenesis for the high-risk HPVs. Through the action of the HPV E7 protein, the G 1 -S checkpoint is bypassed in infected cells by the inactivation of the retinoblastoma tumor suppressor protein (pRB1) (17,18,46). This results in a cellular environment that is conducive to the replication of the viral DNA but in which proapoptotic signals have been triggered. One crucial function of high-risk HPV E6 proteins is to counteract the effects of p53 following this trigger, and this is accomplished by the targeted ubiquitylati...