Cryo-EM structure of the I923V MDA5-dsRNA filament with ADP-AlF4 bound and 73-degree helical twist
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7BKP | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 14.001 |
| f_angle_d | 0.572 |
| f_chiral_restr | 0.039 |
| f_plane_restr | 0.006 |
| f_bond_d | 0.003 |
| Sample |
|---|
| Mouse MDA5 I923V in complex with double stranded RNA |
| Sample Components |
| Mouse MDA5 I923V |
| double stranded RNA |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | 2-4 s blotting, 15 s wait time |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 53484 |
| Reported Resolution (Å) | 3.86 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 42.78 |
| Angular Rotation | 73.94 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7BKP) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | 50 | ||||
| Fitting Procedure | |||||
| Details | Initial local fitting with Fit-in-Map in Chimera followed by real space refinement in Phenix. | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 44 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 500 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | DARK FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | crYOLO | |
| IMAGE ACQUISITION | EPU | 3 |
| CTF CORRECTION | CTFFIND | 4.1 |
| MODEL FITTING | UCSF Chimera | |
| INITIAL EULER ASSIGNMENT | RELION | 4.0 |
| FINAL EULER ASSIGNMENT | RELION | 4.0 |
| CLASSIFICATION | RELION | 4.0 |
| RECONSTRUCTION | RELION | 4.0 |
| MODEL REFINEMENT | PHENIX | 1.21 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 1406812 | |||
