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Homology model of E3 protein of Venezuelan Equine Encephalitis Virus TC-83 strain fitted with a cryo-EM map
by single particle (icosahedral) reconstruction, at 4.8 A resolution
#1: Biological unit as complete icosahedral assembly, Made by Jmol
#2: Biological unit as icosahedral pentamer, Made by Jmol
#3: Biological unit as icosahedral 23 hexamer, Made by Jmol
#4: Depositted structure unit, Made by Jmol
#5: Superimposing with simplified surface model of EM map, EMDB-5275, Made by Jmol
#6: With PDB-3j0c, Made by Jmol
#7: Superimposing with EM 3D map: EMDB-5275 (with PDB-3j0c), Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3j0g |
|---|---|
| Title | Homology model of E3 protein of Venezuelan Equine Encephalitis Virus TC-83 strain fitted with a cryo-EM map |
| Descriptor | E3 protein (E.C.3.4.21.90) |
| Keywords |  VIRUS, alphavirus, bioweapon, VEEV |
| Authors | Zhang, R., Hryc, C.F., Chiu, W. |
| Date | Deposition: 2011-07-21, Release: 2011-08-24 |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Structure Visualization | |
| Movies |  Movie Page#1: Biological unit as complete icosahedral assembly, Made by Jmol #2: Biological unit as icosahedral pentamer, Made by Jmol #3: Biological unit as icosahedral 23 hexamer, Made by Jmol #4: Depositted structure unit, Made by Jmol #5: Superimposing with simplified surface model of EM map, EMDB-5275, Made by Jmol #6: With PDB-3j0c, Made by Jmol #7: Superimposing with EM 3D map: EMDB-5275 (with PDB-3j0c), Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: target map of fitting |
 Article | |
| Citation - primary | |
| Article | EMBO J., Vol. 30, Issue 18, Page 3854-63, Year 2011 |
|---|---|
| Title | 4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus. |
| Authors | Rui Zhang, Corey F Hryc, Yao Cong, Xiangan Liu, Joanita Jakana, Rodion Gorchakov, Matthew L Baker, Scott C Weaver, Wah Chiu Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA. |
| Keywords | Animals, Cryoelectron Microscopy, Encephalitis Virus, Venezuelan Equine (ultrastructure), Horses, Models, Molecular, Viral Proteins (ultrastructure), Viral Vaccines, Virion (ultrastructure), Virulence |
| Links | DOI: 10.1038/emboj.2011.261, PubMed: 21829169, PMC: PMC3173789 |
 Components | |
| ID 1 : Spike glycoprotein E3 | |
| Image |   |
|---|---|
| Description | E3 protein |
| Type | polymer |
| Fragment | UNP residues 276-334 |
| Formula weight | 6488.640 Da |
| Number of molecules | 4 |
| Source | Method: Isolated from a natural source Common name: VEEV Details: purified from infected Baby hamster kidney (BHK) cells NCBI taxonomy: ID:11037Organism scientific: Venezuelan equine encephalitis virus Strain: TC-83 |
| Links | UniProt: P05674, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Details | The virus contains 240 copies of E1, E2, E3 and capsid proteins |
| Name | Venezuelan Equine Encephalitis Virus TC-83 Strain |
| Entity assembly | |
| Name | Venezuelan Equine Encephalitis Virus TC83 strain E3 protein that is cleaved from p62 protein |
| Virus entity | |
| Empty | NO |
| Enveloped | YES |
| Ictvdb id | 00.073.0.01 |
| Virus host category | VERTEBRATES |
| Virus host growth cell | Baby Hamster Kidney cells |
| Virus host species | Equus |
| Virus isolate | STRAIN |
| Virus type | VIRION |
| Buffer | |
| Name | TEN buffer |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 7.4 |
| Sample support | |
| Details | two of the eight grids used for imaging contained continuous carbon film underneath the samples |
| Vitrification | |
| Cryogen name | ETHANE |
| Details | vitrification carried out in Chiu lab, Houston, TX |
| Humidity | 100 |
| Instrument | Vitrobot (FEI Inc) |
| Method | 2 blots, each blot 2 second before plunging, offset = 0 |
| Temp | 89.34 Kelvin |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: JEOL 3200FSC |
|---|---|
| Date | 2008-04-09 |
| Details | omega energy filter |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 300 kV |
| Electron dose | 18 e/A**2 |
| Illumination mode | FLOOD BEAM |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | nominal: 100000 X |
| Cs | nominal: 4.3 mm |
| Astigmatism | objective lens astigmatism was corrected at 100,000 times magnification |
| Nominal defocus | max: 2500 nm, min: 400 nm |
| Energy filter | Omega Filter |
| Specimen holder | |
| Specimen holder | model: JEM3200FSC CRYOHOLDER, type: Eucentric |
| Tilt angle | min: 0.0 degrees, max: 0.0 degrees |
| Temperature | 96 Kelvin |
| Detector | |
| Type | Gatan 4kx4k CCD Camera |
 Processing | |
| 2D projection selection | |
| Software name | CHIMERA |
|---|---|
| Single particle entity | |
| Symmetry type | ICOSAHEDRAL |
| 3D reconstruction | |
| CTF correction method | CTF parameters were determined from particles within each CCD image |
| 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. |
| Euler angles details | The structure was further refined with EMAN1 using the standard projection matching method with progressively decreasing angular step size (with a final value of 0.4 degrees). |
| Method | projection matching |
| Nominal pixel size | 1.07 A/pix |
| Num class averages | 3328 |
| Number of particles | 37000 |
| Resolution | 4.8 A |
| Software | EMAN |
| 3D fitting | |
| Details | The E3 homology model was not further refined against the cryo-EM density map due to its less-resolved quality |
| Method | rigid-body fitting |
| Refinement Space | REAL |
| Software name | CHIMERA |
| Refine hist | |
| Total atoms | 1800 |
| Protein atoms | 1800 |
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