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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
3J0C
pdb_00003j0c
10.2210/pdb3j0c/pdb
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FASTA
PDB
MMCIF
Binary MMCIF
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Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Venezuelan Equine Encephalitis Virus TC-83 Strain
Specimen Preperation
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 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
Map-Model Fitting and Refinement
ID
1
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 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
Date of Experiment
2008-04-09
Temprature (Kelvin)
Microscope Model
JEOL 3200FSC
Minimum Defocus (nm)
400
Maximum Defocus (nm)
2500
Minimum Tilt Angle (degrees)
0.0
Maximum Tilt Angle (degrees)
0.0
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
Imaging Experiment
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
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