Fig. 4: A generalized catalytic core for UBE2R-mediated poly-ubiquitin chain formation.
From: Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases
a, Ribbon diagram of neddylated CUL1–RBX1 bound to SKP1–FBXW7 with trapped UBE2R2~ubiquitin covalently bonded to ubiquitin-primed cyclin E peptide substrate and corresponding cryo-EM density. SKP1–FBXW7 (PDB 2OVP), CUL1 (PDB 6TTU) and the catalytic core (UBE2R2~UBD–UBA–RBX1, this study) were fit into the density using rigid-body refinement (UCSF Chimera). b, Bar graph comparing the ubiquitin transfer rates (kobs) for neddylated CRL1 and CRL2 complexes (substrate receptor identities are indicated on the x axis). The value of each bar represents the estimated value of kobs based on n = 3 technical replicates. c, Same as b except with cyclin E peptide–ubiquitin substrate and neddylated CRL1FBXW7 in combination with the indicated proteins. d, Ribbon diagram of neddylated CUL2–RBX1 bound to Elongin B/C–VHL with trapped UBE2R2~ubiquitin covalently bonded to ubiquitin-primed BRD4 neo-substrate in the presence of the PROTAC MZ1 and corresponding cryo-EM density. Elongin B/C–VHL–MZ1 (PDB 5T35), CUL2 and the catalytic core (this study) were fit into the density as described above. e, Same as c, except with neddylated CRL2VHL, ubiquitin-primed BRD4 neo-substrate (see Methods) and MZ1. UBD, donor ubiquitin; UBA, acceptor ubiquitin; ELOB, Elongin B; ELOC, Elongin C.
