|Entry||Database: EMDB / ID: 5276|
|Title||4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezuelan Equine Encephalitis Virus|
|Keywords||alphavirus / bioweapon / cryoEM / modeling / VEEV|
|Sample||Venezuelan Equine Encephalitis Virus TC-83 Strain|
|Source||Venezuelan equine encephalitis virus / virus / VEEV / ベネズエラウマ脳炎ウイルス|
|Map data||This is a non-icosahedrally averaged map of Venezuelan Equine Encephalitis Virus from the 4 unique sets of E1-E2-E3-CP molecules within one asymmetric unit of the original 3D density map.|
|Method||single particle reconstruction, at 4.8 Å resolution|
|Authors||Zhang R / Hryc CF / Cong Y / Liu X / Jakana J / Gorchakov R / Baker ML / Weaver SC / Chiu W|
|Citation||EMBO J., 2011, 30, 3854-3863|
|Validation Report||PDB-ID: 3j0c|
About validation report
|Date||Deposition: Apr 15, 2011 / Header (metadata) release: Apr 19, 2011 / Map release: Aug 16, 2011 / Last update: Sep 19, 2012|
Downloads & links
|File||emd_5276.map.gz (map file in CCP4 format, 27649 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.07 Å|
CCP4 map header:
-Entire Venezuelan Equine Encephalitis Virus TC-83 Strain
|Entire||Name: Venezuelan Equine Encephalitis Virus TC-83 Strain|
Details: The viruses were purified from infected Baby hamster kidney (BHK) cells
Number of components: 4 / Oligomeric State: E1-E2-E3-CP complex
|Mass||Theoretical: 52 MDa|
-Component #1: virus, Venezuelan equine encephalitis virus
|Virus||Name: Venezuelan equine encephalitis virus / a.k.a: VEEV / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN|
|Mass||Theoretical: 52 MDa|
|Species||Species: Venezuelan equine encephalitis virus / virus / VEEV / ベネズエラウマ脳炎ウイルス|
|Source (natural)||Host Species: Equus caballus / mammal / ウマ / / Host category: VERTEBRATES|
|Sample solution||pH: 7|
|Support film||400 mesh Quantifoil R 1.2/1.3 copper grids|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Method: 2 blots, each blot 2 seconds before plunging / Details: Vitrification instrument: Vitrobot|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 3200FSC / Date: Apr 9, 2008|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 100000 X (nominal)|
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 4.3 mm / Imaging mode: BRIGHT FIELD / Defocus: 400 - 2500 nm / Energy filter: Omega Filter
|Specimen Holder||Holder: Eucentric / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 96 K|
|Camera||Detector: GENERIC GATAN (4k x 4k) / Distance: 200|
|Image acquisition||Number of digital images: 4000 / Details: 4kx4k CCD Image|
|Processing||Method: single particle reconstruction / Number of class averages: 1000 / Number of projections: 37000|
Details: The virus particles were automatically boxed out using ethan, among which around 10,000 particles contained continuous carbon film.
|3D reconstruction||Algorithm: projection matching / Software: EMAN / CTF correction: Each frame|
Details: This is a non-icosahedrally averaged map of Venezuelan Equine Encephalitis Virus from the 4 unique sets of E1-E2-E3-CP molecules within one asymmetric unit of the original 3D density map
Resolution: 4.8 Å / Resolution method: FSC 0.5
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Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
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External links: The 2017 Nobel Prize in Chemistry - Press Release
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