Structure of a mammalian 80S ribosome obtained by docking homology models of the RNA and proteins into an 8.7 A cryo-EM map
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1J5E | |
| experimental model | PDB | 1VI6 | |
| experimental model | PDB | 1FJG | |
| experimental model | PDB | 1IGV | |
| experimental model | PDB | 1I6U | |
| experimental model | PDB | 2AVY | |
| experimental model | PDB | 1G1X | |
| experimental model | PDB | 1RQ6 | |
| experimental model | PDB | 1K7K | |
| Sample |
|---|
| 40S ribosomal subunit in the 80S ribosome-channel complex |
| Sample Components |
| 40S ribosomal subunit |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | plunge freezing with a custom apparatus at 4C and RH greater than 90 percent |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 78800 |
| Reported Resolution (Å) | 8.7 |
| Resolution Method | |
| Other Details | Refinements done in EMAN |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1J5E, 1VI6, 1FJG, 1IGV, 1I6U, 2AVY, 1G1X, 1RQ6, 1K7K) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Rigid body fitting and best visual fit using the program O for RNA. For the proteins DOPE score and other statistical techniques were used to evaluate the best fold and a local exhaustive exploration of Euler angles was used to evaluate the best fit into the density. | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFINEMENT PROTOCOL--Rigid body | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | KODAK SO-163 FILM | ||||||||
| Electron Dose (electrons/Å**2) | 15 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2002-04-01 |
| Temperature (Kelvin) | 93 |
| Microscope Model | FEI TECNAI F20 |
| Minimum Defocus (nm) | 1100 |
| Maximum Defocus (nm) | 4400 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | 50000 |
| Calibrated Magnification | 51000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| CTF CORRECTION | CTFFIND | 3 |
| MODEL FITTING | Insight II | |
| MODEL FITTING | Mod-EM | |
| MODEL FITTING | MODPIPE | |
| MODEL FITTING | O | |
| MODEL FITTING | RSRef | |
| RECONSTRUCTION | RELION | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| CTF correction using phase flipping and setsf in EMAN to correct the amplitudes | ||||
