The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD-CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences for different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein-E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.cell cycle | tumor suppressor protein | E2F | protein-protein interactions | evolution E 2F transcription factors regulate the mammalian cell cycle by controlling expression of genes required for DNA synthesis and cell division (1). E2F activity is regulated by the retinoblastoma (Rb) "pocket" protein family members Rb, p107, and p130, which bind and inhibit E2F and recruit repressive factors to E2F-driven promoters (2-5). Beyond cell-cycle regulation, these pocket protein-E2F complexes are the focal point of signaling pathways that trigger diverse cellular processes including proliferation, differentiation, apoptosis, and the stress response. Improper inactivation of pocket proteins is a common mechanism by which cancerous cells maintain aberrant proliferation (1, 5-7). Pocket protein-E2F dissociation and subsequent E2F activation is induced by cyclindependent kinase phosphorylation (3-5, 8) or binding of viral oncoproteins such as the SV40 T-antigen (9).The E2F family contains eight members, five of which (E2F1 to E2F5) form complexes with pocket proteins (1). E2F1 to E2F3 associate exclusively with Rb and are potent activators of transcription during the G1 and S phases of the cell cycle (10, 11). These "activating" E2Fs also specifically induce apoptosis (12). E2F4 is found in complexes with all three pocket proteins and is thought of primarily as a repressor, because it typically occupies promoters of repressed genes and is exported from the nucleus upon release from pocket proteins (1,13,14). In contrast, several studies of E2F4 function during development suggest that E2F4 may stimulate proliferation in certain contexts, acting through association with other transcription factors (14). Better characterization of how E2F4 and E2F5 associate with pocket proteins and other factors is needed to unde...