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- EMDB-5276: 4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezue... -

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Basic information

Entry
Database: EMDB / ID: 5276
Title4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezuelan Equine Encephalitis Virus
Keywordsalphavirus / bioweapon / cryoEM / modeling / VEEV
SampleVenezuelan Equine Encephalitis Virus TC-83 Strain
SourceVenezuelan equine encephalitis virus / virus / VEEV / ベネズエラウマ脳炎ウイルス
Map dataThis 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.
Methodsingle particle reconstruction, at 4.8 Å resolution
AuthorsZhang R / Hryc CF / Cong Y / Liu X / Jakana J / Gorchakov R / Baker ML / Weaver SC / Chiu W
CitationEMBO J., 2011, 30, 3854-3863

EMBO J., 2011, 30, 3854-3863 StrPapers
4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus.
Rui Zhang / Corey F Hryc / Yao Cong / Xiangan Liu / Joanita Jakana / Rodion Gorchakov / Matthew L Baker / Scott C Weaver / Wah Chiu

Validation ReportPDB-ID: 3j0c

SummaryFull report
PDB-ID: 3j0g

SummaryFull report
About validation report
DateDeposition: Apr 15, 2011 / Header (metadata) release: Apr 19, 2011 / Map release: Aug 16, 2011 / Last update: Apr 15, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 6
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-3j0c
  • Surface level: 6
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_5276.map.gz (map file in CCP4 format, 27649 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.07 Å/pix.
= 205.44 Å
192 pix
1.07 Å/pix.
= 205.44 Å
192 pix
1.07 Å/pix.
= 205.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour Level:6 (by author), 6 (movie #1):
Minimum - Maximum-13.58756733 - 32.44748688
Average (Standard dev.)-0.00455169 (0.93261677)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin32-47-297
Limit223144-106
Spacing192192192
CellA=B=C: 205.44 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z205.440205.440205.440
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-4732-297
NC/NR/NS192192192
D min/max/mean-13.58832.447-0.005

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Supplemental data

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Sample components

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Entire Venezuelan Equine Encephalitis Virus TC-83 Strain

EntireName: 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
MassTheoretical: 52 MDa

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Component #1: virus, Venezuelan equine encephalitis virus

VirusName: Venezuelan equine encephalitis virus / a.k.a: VEEV / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
MassTheoretical: 52 MDa
SpeciesSpecies: 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

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7
Support film400 mesh Quantifoil R 1.2/1.3 copper grids
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Method: 2 blots, each blot 2 seconds before plunging / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC / Date: Apr 9, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 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 HolderHolder: Eucentric / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 96 K
CameraDetector: GENERIC GATAN (4k x 4k) / Distance: 200

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Image acquisition

Image acquisitionNumber of digital images: 4000 / Details: 4kx4k CCD Image

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Image processing

ProcessingMethod: 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 reconstructionAlgorithm: 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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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: Rigid Body
Input PDB model: 3N40
Output model

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