4V5Z
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) | |||
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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 |
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40S ribosomal subunit in the 80S ribosome-channel complex |
Sample Components |
40S ribosomal subunit |
Specimen Preparation | |
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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 | |
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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 | |||||
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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 | |||||||||
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Detector Type | KODAK SO-163 FILM | ||||||||
Electron Dose (electrons/Å**2) | 15 |
Imaging Experiment | 1 |
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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 | ||
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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 | ||||
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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 |