Table 1 Cryo-EM data collection, refinement and validation statistics and atomic models for the 26S proteasome with excess TXNL1 at 2 min after adding FAT10–Eos substrate and NUB1 cofactor
From: Structural landscape of the degrading 26S proteasome reveals conformation-specific binding of TXNL1
PSRpt2 + TXNL1 bound to partially folded Eos (RP refined) | PSRpt5 + TXNL1 | PSRpt1 + TXNL1 | PSRpt4 + TXNL1 | RS + TXNL1 Forward | RS + TXNL1 Backward | PSRpt2 + TXNL1 (Eos resolved, AAA+ local) | |
|---|---|---|---|---|---|---|---|
EM Data Bank | EMD-47726 | EMD-47719 | EMD-47722 | EMD-47724 | EMD-47721 | EMD-47720 | EMD-71534 |
PDB | |||||||
Dataset | 26S proteasome with excess TXNL1, FAT10–Eos and NUB1 incubated for 120 s | ||||||
Magnification | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 | ×81,000 |
Voltage (kV) | 300 | 300 | 300 | 300 | 300 | 300 | 300 |
Electron exposure (e− per Å2) | 50 | 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 | −0.7 to −2.0 |
Pixel size (Å) | 1.048 | 1.048 | 1.048 | 1.048 | 1.048 | 1.048 | 1.048 |
Symmetry imposed | C1 | C1 | C1 | C1 | C1 | C1 | C1 |
Initial particles (n) | 1,410,257 | 1,410,257 | 1,410,257 | 1,410,257 | 1,410,257 | 1,410,257 | 1,410,257 |
Final particles | 73,136 | 95,431 | 19,309 | 29,525 | 62,431 | 53,010 | 73,136 |
Map resolution (Å) FSC threshold | 3.1 0.143 | 3.01 0.143 | 3.47 0.143 | 3.59 0.143 | 2.87 0.143 | 2.9 0.143 | 2.98 0.143 |
Refinement | |||||||
Model resolution (Å) FSC threshold | 3.1 0.5 | 2.9 0.5 | 3.4 0.5 | 3.5 0.5 | 2.8 0.5 | 2.8 0.5 | 2.9 0.5 |
Map sharpening B factor (Å2) (determined) | −50.5 | −50.4 | −27 | −29.9 | −47.2 | −45.3 | −49.6 |
Initial model used (PDB) | |||||||
Nonhydrogen atoms | 83,181 | 82,194 | 70,858 | 70,522 | 71,304 | 71,304 | 33,552 |
Residues | 10,532 | 10,415 | 8,967 | 8,939 | 8,986 | 8,986 | 4,241 |
Ligands | Zn2+: 1 Mg2+: 3 ATP: 2 ADP: 4 CR8: 1 | Zn2+: 1 Mg2+: 5 ATP: 3 ADP: 3 UNK: 12 | Zn2+: 1 Mg2+: 5 ATP: 4 ADP: 2 UNK: 10 | Zn2+: 1 Mg2+: 3 ATP: 2 ADP: 4 UNK: 13 | Zn2+:1 Mg2+:6 ATP:5 ADP:1 | Zn2+: 1 Mg2+: 6 ATP: 5 ADP: 1 | Zn2+: 1 Mg2+: 3 ATP: 2 ADP: 4 UNK: 22 |
B factors (Å2) (min/max/mean) | |||||||
Protein | 15.62/408.71/134.25 | 28.19/207.68/92.08 | 30.99/177.39/71.82 | 84.71/567.71/186.99 | 9.64/428.56/66.08 | 15.22/376.19/65.50 | 57.32/299.16/131.17 |
Ligand | 80.74/181.62/114.17 | 43.13/135.11/79.05 | 36.17/70.91/49.10 | 124.90/183.00/155.97 | 26.88/81.49/40.45 | 28.47/84.97/39.91 | 62.24/188.08/121.97 |
Root-mean-square deviation | |||||||
Bond lengths (Å) | 0.006 | 0.005 | 0.006 | 0.005 | 0.004 | 0.004 | 0.005 |
Bond angles (°) | 1.122 | 0.97 | 1.028 | 1.116 | 0.95 | 0.945 | 1.075 |
MolProbity | 2.83 | 1.91 | 3.41 | 2.55 | 1.97 | 1.98 | 2.56 |
Clashscore | 23.77 | 61.18 | 69.78 | 19.63 | 11.89 | 11.58 | 17.98 |
Poor rotamers (%) | 4.53 | 5.17 | 5.61 | 2.69 | 2.36 | 2.45 | 3.09 |
Ramachandran plot | |||||||
Favored (%) | 92.36 | 94.09 | 90.72 | 93.24 | 97.53 | 97.50 | 93.23 |
Allowed (%) | 7.41 | 5.49 | 8.80 | 6.33 | 2.46 | 2.47 | 6.55 |
Disallowed (%) | 0.23 | 0.42 | 0.47 | 0.43 | 0.01 | 0.03 | 0.21 |
