6I3M

eIF2B:eIF2 complex, phosphorylated on eIF2 alpha serine 52.

ELECTRON MICROSCOPY

Sample
Complex of translation initiation factors eIF2 and eIF2B

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK III
Cryogen Name	ETHANE
Sample Vitrification Details	Blot for 2 seconds before plunging

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	64541
Reported Resolution (Å)	3.93
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (5B04, 3JAP)	2 (3JAP, 3JAP, 3JAP)
Refinement Space	REAL	REAL
Refinement Protocol	FLEXIBLE FIT	RIGID BODY FIT
Refinement Target	correlation coeficient	Cross-correlation coefficient
Overall B Value
Fitting Procedure
Details	Modeller was used to build homology model of S. cerevisiae eIF2B structure based on S. pombe crystal structure. Subunits of the homology model, along ...	Modeller was used to build homology model of S. cerevisiae eIF2B structure based on S. pombe crystal structure. Subunits of the homology model, along with eIF2 alpha domains 1 and 2, were then rigid body fitted into our map using UCSF Chimera. The model then was refined using phenix and manually adjusted in Coot.	eIF2 alpha domain 3, eIF2 gamma, and eIF2 beta (3JAP) were rigid body fitted into our map using Chimera.

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	40

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	4000
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
Calibrated Magnification	37313
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Tilt at zero and 35 degrees.

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	2.01
IMAGE ACQUISITION	EPU
CTF CORRECTION	Gctf
MODEL FITTING	MODELLER
MODEL FITTING	UCSF Chimera
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	RELION	2.1
FINAL EULER ASSIGNMENT	RELION	2.1
CLASSIFICATION	RELION	2.1
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX
MODEL FITTING	UCSF Chimera

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTF determination was performed per micrograph initially. After particle picking and initial reconstruction, per particle CTF determination was performed.	655000	Initially, approximately 3000 particles were picked manually and used for 2D classification. Then 4 best looking 2D class average images were used as references for automated particle picking in RELION. For the zero tilt data collection, 406000 particles were picked. For the 35 degree tilt data collection, 249000 particles were picked

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.