3J0C | pdb_00003j0c

Models of E1, E2 and CP of Venezuelan Equine Encephalitis Virus TC-83 strain restrained by a near atomic resolution cryo-EM map

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N40
experimental model	PDB	1EP5

Sample
Venezuelan Equine Encephalitis Virus TC-83 Strain
Sample Components
Venezuelan Equine Encephalitis Virus TC83 strain E1 protein
Venezuelan Equine Encephalitis Virus TC83 strain E2 protein
Venezuelan Equine Encephalitis Virus TC83 strain capsid 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	FSC 0.5 CUT-OFF
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)	2 (3N40)	3 (1EP5)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--all-atom refinement REFINEMENT PROTOCOL--all-atom refinement against cryo-EM density DETAILS--ROSETTA was used to refine the full-length E1 a ...	METHOD--all-atom refinement REFINEMENT PROTOCOL--all-atom refinement against cryo-EM density DETAILS--ROSETTA was used to refine the full-length E1 and E2 and all of the structured part of CP. ROSETTA uses the cryo-EM density as a restraint, along with energy minimization, to eliminate steric clashes and assure proper molecular geometry.

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	Rosetta
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 R01GM157729.