ELECTRON MICROSCOPY

Sample

Late-stage 48S Initiation Complex (LS48S IC) guided by the trans-RNA of 15 nt length, purification method of biotinylated DNA-oligo pull-down

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK IV
Cryogen Name ETHANE
Sample Vitrification Details The sample was incubated on the grid for 30 s and then blotted with filter paper from both sides for 1.5 s with the blot force 5
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 1000
Reported Resolution (Å) 2.9
Resolution Method OTHER
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space ?
Refinement Protocol RIGID BODY FIT
Refinement Target ?
Overall B Value ?
Fitting Procedure ?
Details The atomic model of LS48S IC complex (PDB: 8P09) was initially rigid body fitted in density using ChimeraX and further model building was done for mRNA, eIF5 N-terminal domain, eIF2gamma, eIF3d and eIF3 octamer in ChimeraX. Densities for eIF5 N-terminal domain, eIF2gamma, eIF3d and eIF3 octamer were observed in the map and therefore were included in the model. The 3D structure of the eIF5-N terminal domain was generated by Alphafold2 (PDB: G1TGW1). It was then accommodated into the model by aligning structurally to its counterparts in the yeast atomic model of the py48S-eIF5N pre-initiation complex (PDB: 6FYX). IF3d and eIF3 octamer were taken from the atomic model of LS48S IC complex with eIF3 proteins (PDB: 6YAM) and placed into density by rigid-body fitting. The atomic models with and without eIF3 proteins were inspected visually and performed stereochemical, torsional, angle refinement and optimization by using ISOLDE v1.6. Figures featuring cryo-EM densities and atomic models were visualized by using ChimeraX.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 50
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TALOS ARCTICA
Minimum Defocus (nm) 500
Maximum Defocus (nm) 2500
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS 2.7
Imaging Mode BRIGHT FIELD
Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification 59000
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 200
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION cryoSPARC 4.5.1
IMAGE ACQUISITION SerialEM 4.1
CTF CORRECTION CTFFIND 4
MODEL FITTING UCSF ChimeraX 1.8
MODEL REFINEMENT ISOLDE 1.6
MODEL REFINEMENT PHENIX 1.20.1-4487
RECONSTRUCTION cryoSPARC 4.5.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
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