ISDA: 9H74

ELECTRON MICROSCOPY

Sample

Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 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	?

Feedback Form