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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
    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 A 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

    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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    Map

    Fileemd_5276.map.gz (map file in CCP4 format, 27649 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    192 pix
    1.07 A/pix
    = 205.44 A
    192 pix
    1.07 A/pix
    = 205.44 A
    192 pix
    1.07 A/pix
    = 205.44 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.07 A
    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 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/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
    alpha/beta/gamma90.00090.00090.000
    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
    Source (natural)Host Species: Equus caballus / mammal / / 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/A2 / 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 A / 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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