Table 2.
Cryo-EM data collection, refinement, and validation statistics
| YaxAB (20-mer) (EMDB-3885) (PDB-6EL1) |
|
|---|---|
| Data collection and processing | |
| Magnification | 59,000 |
| Voltage (kV) | 300 |
| Electron exposure (e–/Å2) | 60 |
| Defocus range (μm) | 1.1–2.5 |
| Pixel size (Å) | 1.106 |
| Symmetry imposed | C10 |
| Initial particle images (no.) | 178,149 |
| Final particle images (no.) | 24,822 |
| Map resolution (Å) | 6.1 |
| FSC threshold | 0.143 |
| Map resolution range (Å) | 4.8–7.0 |
| Refinement | |
| Initial model used (PDB code) | 6EK7, 6EK8 |
| Model resolution (Å) | 6.1 |
| FSC threshold | 0.143 |
| Model resolution range (Å) | 4.8–7.0 |
| Map sharpening B-factor (Å2) | −331 |
| Model composition | |
| Protein residues | 6830 |
| B-factors (Å2) | |
| Protein | 322 |
| R.m.s. deviations | |
| Bond lengths (Å) | 0.005 |
| Bond angles (°) | 0.93 |
| Validation | |
| MolProbity score | 1.87 |
| Clashscore | 7.4 |
| Poor rotamers (%) | 0.5 |
| Ramachandran plot | |
| Favored (%) | 92.5 |
| Allowed (%) | 7.5 |
| Disallowed (%) | 0 |
The Yersinia YaxAB system is a pore-forming toxin of so far unknown structure. Here authors present X-ray and cryo-EM to structures of individual subunits and of the YaxAB pore complex, and find that YaxA binds to membranes first and recruits YaxB for subsequent oligomerization