Cryo-EM structure of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub.
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6MSB | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 14.672 |
| f_angle_d | 0.997 |
| f_chiral_restr | 0.056 |
| f_bond_d | 0.011 |
| f_plane_restr | 0.007 |
| Sample |
|---|
| Human 26S proteasome |
| Sample Components |
| 19S regulatory particle (RP) of human 26S proteasome |
| AAA+-ATPase of 19S regulatory particle (RP) of human 26S proteasome |
| alpha subunits of the 20S core particle (CP) of human 26S proteasome |
| K11/K48-branched ubiquitin (Ub) chain composed of four Ub. |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | incubation time= 3 s blotting time= 2.5 s |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 52216 |
| Reported Resolution (Å) | 3.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Performed in cryoSPARC using Non-uniform Refinment job type. Some parts of the map were then improved by using focused local refinement. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6MSB) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | 0.83 | ||||
| Overall B Value | 110.45 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 49 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1200 |
| Maximum Defocus (nm) | 1800 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 70000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Topaz | |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | 4.1 |
| MODEL FITTING | UCSF ChimeraX | 1.3 |
| MODEL REFINEMENT | ISOLDE | 1.3 |
| MODEL REFINEMENT | Coot | 0.9.4.1 EL |
| MODEL REFINEMENT | PHENIX | 1.19.2 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 3.1 |
| CLASSIFICATION | cryoSPARC | 3.1 |
| RECONSTRUCTION | cryoSPARC | 3.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 2695911 | |||
