Extended Data Fig. 9: Conservation of pocket domain structure and linear motif binding sites across mammalian pocket proteins.

a, Structural conservation of the pocket domain across mammalian pocket proteins. The human Rb pocket domain (PDB:1GUX) is shown aligned with 9 structural models of Rb pocket domains from representative mammalian species plus the human paralogs p107 (PDB:4YOZ) and p130. The models of the Rb pocket domains and p130 were obtained by using Alphafold2 implemented in ColabFold (See Methods). Secondary structure is depicted in rainbow colors. The E2F (left) and LxCxE (right) motifs are depicted as green ribbons (PDB 2R7G and 1GUX respectively). b, Structural conservation of the E2F and LxCxE clefts in pocket proteins. Structural alignment shown in panel A with the residues that mediate binding to the E2F and LxCxE motifs (marked as asterisks in Supplementary Fig. 1) depicted as blue and red sticks respectively. c, The distance between the E2F and LxCxE binding sites is highly conserved across mammalian pocket proteins. The spacing was measured between the C-terminal anchor site of the E2F cleft (blue sphere) and the N-terminal anchor site of the LxCxE cleft (red sphere). Distances are: 46.0 Å (human, macaque and chicken), 46.1 Å (chimpanzee, dog, microbat, cow, sheep, pig, horse and tree shrew), 47.3 Å (p107) and 46.5 Å (p130). These distances are slightly shorter than the distance between binding sites used in the C_eff calculations (r₀ = 49 Å), which was measured between the C-terminal residue of the E2F motif and the N-terminal residue of the LxCxE motif using the structures of the motifs bound to Rb (PDB: 2R7G and 1GUX).