Table 2 Cryo-EM data collection, refinement and validation statistics and atomic models for the 26S proteasome at 30 s after adding FAT10–Eos substrate and NUB1 cofactor
From: Structural landscape of the degrading 26S proteasome reveals conformation-specific binding of TXNL1
PSRpt3+ (AAA+ local) | PSRpt6 (AAA+ local) | PSRpt4 (AAA+ local) | PSRpt5 (AAA+ local) | PSRpt1 (AAA+ local) | PSRpt2 (AAA+ local) | |
|---|---|---|---|---|---|---|
EM Data Bank | EMD-47725 | EMD-47723 | EMD-71584 | EMD-71537 | EMD-71538 | EMD-47727 |
PDB | ||||||
Dataset | 26S proteasome with FAT10–Eos substrate and NUB1 cofactor incubated for 30 s | |||||
Magnification | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e− per Å2) | 50 | 50 | 50 | 50 | 50 | 50 |
Defocus range (μm) | −0.7 to −2.0 | −0.7 to −2.0 | −0.7 to −2.0 | −0.7 to −2.0 | −0.7 to −2.0 | −0.7 to −2.0 |
Pixel size (Å) | 1.048 | 1.048 | 1.048 | 1.048 | 1.048 | 1.048 |
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 |
Initial particles (n) | 1,159,433 | 1,159,433 | 1,159,433 | 1,159,433 | 1,159,433 | 1,159,433 |
Final particles | 15,623 | 10,722 | 16,398 | 66,749 | 26,687 | 31,377 |
Map resolution (Å) FSC threshold | 3.62 0.143 | 4.08 0.143 | 3.68 0.143 | 2.76 0.143 | 3.06 0.143 | 3.16 0.143 |
Refinement | ||||||
Model resolution (Å) FSC threshold | 3.4 0.5 | 3.9 0.5 | 3.4 0.5 | 2.7 0.5 | 3 0.5 | 3.1 0.5 |
Map sharpening B factor (Å2) (determined) | −35.2 | −25.6 | −34.6 | −48.1 | −35.6 | −43 |
Initial model used (PDB) | ||||||
Nonhydrogen atoms | 32,822 | 31,852 | 32,711 | 33,269 | 33,115 | 80,403 |
Residues | 4,201 | 4,080 | 4,184 | 4,224 | 4,224 | 10,175 |
Ligands | Zn2+: 1 Mg2+: 2 ATP: 2 ADP: 4 UNK: 14 | Zn2+: 1 Mg2+: 2 ATP: 2 ADP: 4 UNK: 8 | Zn2+: 1 Mg2+: 2 ATP: 2 ADP: 4 UNK: 12 | Zn2+: 1 Mg2+: 5 ATP: 3 ADP: 3 UNK: 11 | Zn2+: 1 Mg2+: 5 ATP: 4 ADP: 2 UNK: 11 | Zn2+: 1 Mg2+: 3 ATP: 2 ADP: 4 UNK: 22 |
B factors (Å2) (min/max/mean) | ||||||
Protein | 64.75/308.37/159.51 | 30.00/191.54/68.65 | 30.00/224.88/72.43 | 43.03/262.47/116.41 | 36.83/232.66/98.36 | 4.70/325.03/155.52 |
Ligand | 86.08/201.04/121.76 | 20.00/276.72/79.74 | 20.00/183.00/64.68 | 54.42/266.33/94.96 | 43.25/130.03/74.14 | 15.67/202.00/77.12 |
Root-mean-square deviation | ||||||
Bond lengths (Å) | 0.004 | 0.005 | 0.005 | 0.005 | 0.004 | 0.005 |
Bond angles (°) | 0.9 | 1.104 | 1.112 | 1.047 | 1.028 | 1.129 |
MolProbity | 2.66 | 2.25 | 2.64 | 2.43 | 2.44 | 2.82 |
Clashscore | 19.66 | 18.44 | 17.76 | 15.21 | 15.32 | 25.68 |
Poor rotamers (%) | 3.24 | 0.06 | 3.57 | 2.57 | 2.91 | 3.85 |
Ramachandran plot | ||||||
Favored (%) | 92.26 | 92.03 | 92.53 | 94.97 | 94.17 | 92.35 |
Allowed (%) | 7.07 | 7.37 | 7.11 | 4.67 | 5.57 | 7.47 |
Disallowed (%) | 0.68 | 0.60 | 0.36 | 0.36 | 0.26 | 0.18 |
