3J0G

Homology model of E3 protein of Venezuelan Equine Encephalitis Virus TC-83 strain fitted with a cryo-EM map

ELECTRON MICROSCOPY

Sample
Venezuelan Equine Encephalitis Virus TC83 strain E3 protein that is cleaved from p62 protein

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details	vitrification carried out in Chiu lab, Houston, TX

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	37000
Reported Resolution (Å)	4.8
Resolution Method
Other Details	After each iteration, the non-icosahedral parts (which included the lipids and the RNA) in the reconstruction were removed by a soft-edged mask derive ...	After each iteration, the non-icosahedral parts (which included the lipids and the RNA) in the reconstruction were removed by a soft-edged mask derived from an icosahedrally organized, protein-only map that was low-pass filtered to 30 Angstroms. This map then served as the reference model for the next iteration.
Refinement Type
Symmetry Type	POINT
Point Symmetry	I

Map-Model Fitting and Refinement
Id	1 (3N40)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--rigid-body fitting DETAILS--The E3 homology model was not further refined against the cryo-EM density map due to its less-resolved quality

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	18

Imaging Experiment	1
Date of Experiment	2008-04-09
Temperature (Kelvin)	96
Microscope Model	JEOL 3200FSC
Minimum Defocus (nm)	400
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	4.3
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	JEOL 3200FSC CRYOHOLDER
Nominal Magnification	100000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	omega energy filter

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	CTF parameters were determined from particles within each CCD image

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.