Table 1 Cryo-EM data collection, refinement and validation statistics
CUL9–RBX1 focused cullin dimer (neddylated + unneddylated) | CUL9–RBX1 hexameric assembly | CUL9–RBX1 focused dimeric core | CUL9–RBX1 focused on E2-like density | CUL9–RBX1 symmetry expanded unneddylated dimer | |
|---|---|---|---|---|---|
CUL9 | WT | WT | WT | WT | WT |
RBX1 | Residues: 5–108 | Residues: 5–108 | Residues: 5–108 | Residues: 5–108 | Residues: 5–108 |
NEDD8 | Endogenous | ||||
E2 | Endogenous | ||||
Accession codes | EMD-18218 | EMD-18217 | |||
Data collection and processing | |||||
Microscope, magnification | Krios, 105,000 | Krios, 105,000 | Krios, 105,000 | Krios, 105,000 | Krios, 105,000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e−/Å2) | ~60 | ~60 | ~60 | ~60 | ~60 |
Defocus range (μm) | ~−0.7 to −2.8 | ~−0.7 to −2.8 | ~−0.7 to −2.8 | ~−0.7 to −2.8 | ~−0.7 to −2.8 |
Pixel size (Å) | 0.8512 | 0.8512 | 0.8512 | 0.8512 | 0.8512 |
Symmetry imposed | C1 | C3 | C1 | C1 | C3 |
Initial particle images (no.) | 1,212,742 | ||||
Final particle images (no.) | 71,928 | 611,252 | 71,928 | 153,970 | 661,706 |
Map resolution (Å) | 4.1 | 4.4 | 3.5 | 4.2 | 3.37 |
FSC threshold | (0.143) | (0.143) | (0.143) | (0.143) | (0.143) |
Map resolution range (Å) | 3.5–9 | 3.6–13 | 2.8–15 | ||
Refinement | |||||
Initial model used (PDB code) | Alphafold Q8IWT37 PDB 7B5L PDB 7Z8B | ||||
Model resolution (Å) | 4.1 | 4.4 | 3.37 | ||
FSC threshold | (0.143) | (0.143) | (0.143) | ||
Model resolution range (Å) | 3.5–9 | 3.6–13 | 2.8–15 | ||
Map sharpening B factor (Å2) | −127 | −150 | −139.7 | ||
Model composition | |||||
Nonhydrogen atoms | 18,033 | 29,815 | 15,223 | ||
Protein residues | 2,932 | 6,016 | 2,439 | ||
Ligands | 10 | 6 | |||
B factors (Å2) | |||||
Protein | 104.9 | 90.8 | 98.28 | ||
Ligand | 296.65 | 252.68 | |||
R.m.s. deviations | |||||
Bond lengths (Å) | 0.005 | 0.005 | 0.008 | ||
Bond angles (°) | 1.009 | 1.071 | 1.033 | ||
Validation | |||||
MolProbity score | 1.34 | 0.84 | 1.67 | ||
Clashscore | 6.13 | 1.23 | 4.73 | ||
Poor rotamers (%) | 0 | 0 | 0.12 | ||
Ramachandran plot | |||||
Favored (%) | 99.21 | 99.4 | 93.47 | ||
Allowed (%) | 0.79 | 0.6 | 6.53 | ||
Disallowed (%) | 0 | 0 | 0 | ||
