Extended Data Fig. 7: Structural features of RF12 and putative interactions of the RFs with E2 enzymes.

a, Overlay of the cryo-EM structure of T. thermophilus (T.t.) RF12 with the crystal structure of S. cerevisiae (S.c.) RF12 (see also Extended Data Table 2). The structures are shown as cartoons with Cys residues as yellow sticks and the bound Zn²⁺ atom as a grey ball. Note that the cores of the structures are similar, but several loops are different. b, Putative interaction between the S. cerevisiae RF10–RF12 complex and an E2–Ub conjugate. The structure of RF10 is a homology model, based on the cryo-EM structure, and that of RF12 a crystal structure (a). The structure of RF10–RF12 was aligned with the structure of the homodimeric RF of the ubiquitin ligase RNF4 bound to the ubiquitin-conjugated E2 enzyme UbcH5a (PDB code 4AP4). The alignment is based on RF10 and one of the RFs in RNF4. UbcH5a and ubiquitin are shown as cartoons inside a semi-transparent space-filling model. RF10 and RF12 are shown as colored cartoons, and the RFs of RNF4 as white cartoons. One circle highlights the linchpin residues of RF10 and RNF4 (R324 and R181, respectively), the other shows the interaction between L398 of Pex12 or the equivalent residue in RNF4 (Y258) with the ubiquitin helix. c, As in b, but for the homodimeric RF ligase BIRC7 (PDB code 4AUQ). d, The modelled structure of an E2~Ub conjugate was docked onto the putative binding site of RF2. The observed clashes suggest that RF2 must undergo a conformational change for its activation. e, As in d, but for the docking of E2–Ub onto RF10. Severe clashes suggest again a conformational change for activation.