Extended Data Figure 5. Extraordinary cullin-RING conformational changes in catalytic architecture juxtaposing substrate and ubiquitylation active site.

a, Side-by-side comparison of relative RING domain locations in different CRL complexes after superposition of the C/R domains from the original CUL1-RBX1 structure (PDB ID 1LDJ, “Pre-Neddylation”, which data herein shows is dynamic, although the crystal structure likely captured the conformation allowing CAND1 binding and substrate receptor exchange)⁷, the structure representing the Neddylation reaction (PDB ID 4P5O)³⁹, and a structure of a neddylated CUL5-RBX1 domain (PDB ID 3DQV, labeled “Post-Neddylation”, which revealed potential for neddylated CUL WHB and RBX1 RING domain conformational changes³, and data herein shows is dynamic), and the structure presented here showing how the neddylated CUL1 WHB domain and RBX1 RING are harnessed in a catalytic architecture for “Active ubiquitylation”. RBX1’s Trp35 is highlighted to show it serving as a multifunctional platform for either the RING domain in different orientations, or for the E2-linked NEDD8 during neddylation³⁹. b, Superposition of the structures shown in a, highlighting different relative RING positions. c, Comparison of CUL WHB domain relative locations after superimposing their C/R domains (not shown). d, Cryo EM density from the neddylated CRL1^β-TRCP-UBE2D~UB-substrate intermediate complex, showing patchiness of region corresponding to CUL1 “Helix-29”⁷. This CUL1 region connecting the C/R and WHB domains is visible only as patchy density, whereas in prior cullin crystals this forms the rod-like Helix-29 continuing into the WHB domain⁷. It seems CUL1’s Helix-29 dissolves into a flexible tether, which rationalizes the previously observed proteolytic sensitivity of this region in a neddylated CUL1-RBX1 complex³, and enables the displacement and rotation required for placing the ensuing WHB domain and its linked NEDD8 at the center of the ubiquitylation complex.