Table 1 Cryo-EM data, map and model statistics of Msn5-RanGTP-pPho41-200 and unliganded Msn5
From: Phosphate-dependent nuclear export via a non-classical NES class recognized by exportin Msn5
Msn5-RanGTP-pPho41-200 | Msn5 (EMD-46548) (PDB 9D43) | |||
|---|---|---|---|---|
State 1-1 (EMD-46549) (PDB 9D45) | State 2-1 (EMD-47291) (PDB 9DXM) | State 3-1 (EMD-47325) (PDB 9DZ6) | ||
Data collection and processing | ||||
Magnification | 105,000 | 81,000 | ||
Voltage (kV) | 300 | 300 | ||
Electron exposure (e–/Å2) | 50 | 50 | ||
Defocus range (μm) | −0.8 to −2.5 | −0.8 to −2.5 | ||
Pixel size (Å) | 0.83 | 1.02885 | ||
Symmetry imposed | C1 | C1 | ||
Initial particle images after 1st clean-up (no.) | 1,574,329 | 4,135,768 | ||
Final particle images (no.) | 102,030 | 102,289 | 112,923 | 1,048,421 |
Map resolution (Å) | 3.08 | 3.19 | 3.11 | 3.39 |
FSC Threshold | 0.143 | 0.143 | 0.143 | 0.143 |
Map resolution range (Å) | 2.62-6.67 | 2.80-6.72 | 2.68-6.16 | 2.89-5.72 |
B factor (Å2) | 89.9 | 90.7 | 89.3 | 174.5 |
Refinement | ||||
Initial model used | Msn5 and RanGTP from 3m1I | SWISS model of 5YU7 | ||
Model resolution (Å) | 2.9/3.0/3.2 | 3.0/3.2/2.3 | 3.0/3.1/3.2 | 3.3/3.4/3.6 |
FSC threshold | 0/0.143/0.5 | 0/0.143/0.5 | 0/0.143/0.5 | 0/0.143/0.5 |
Model composition | ||||
Nonhydrogen atoms | 11123 | 10056 | 10126 | 9754 |
Protein residues | 1354 | 1224 | 1232 | 1189 |
Ligand | 2 (GTP, Mg) | 2 (GTP, Mg) | 2 (GTP, Mg) | 0 |
B factors (Å2) | ||||
Protein | 30.00/469.43/159.44 | 30.00/215.68/113.42 | 30.00/249.07/144.89 | 113.31/378.98/177.57 |
Ligand | 136.33/148.85/143.99 | 133.09/172.98/157.80 | 149.57/184.59/170.08 | - |
R.m.s. deviations | ||||
Bond lengths (Å) | 0.003 | 0.006 | 0.004 | 0.002 |
Bond angles (°) | 0.610 | 0.596 | 0.487 | 0.481 |
Validation | ||||
MolProbity score | 1.33 | 1.26 | 1.35 | 1.53 |
Clashscore | 5.43 | 3.86 | 5.04 | 5.52 |
Poor rotamers (%) | 0.72 | 0.00 | 0.26 | 0.09 |
Ramachandran plot | ||||
Favored (%) | 97.84 | 97.60 | 97.60 | 96.45 |
Allowed (%) | 2.16 | 2.40 | 2.31 | 3.55 |
Disallowed (%) | 0.00 | 0.00 | 0.08 | 0.00 |
Missing residues | Msn5: 1–4, 1165–1224; Ran: 1–9; Pho4: 1–111, 135–200 | Msn5: 1–4, 827–844, 962–977, 1006–1014, 1070–1071, 1087–1100, 1117–1224; Ran: 1–9; Pho4: 1–200 | Msn5: 1–5, 826–845, 962–977, 1003–1016, 1070–1072, 1088–1098, 1118–1119, 1128–1224; Ran: 1–9; Pho4: 1–200 | Msn5: 1–4, 829–834, 1167–1174, 1208–1224 |
