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    - PDB-3j0g: Homology model of E3 protein of Venezuelan Equine Encephalitis Vi... -

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    Basic information

    Entry
    Database: PDB / ID: 3j0g
    TitleHomology model of E3 protein of Venezuelan Equine Encephalitis Virus TC-83 strain fitted with a cryo-EM map
    DescriptorE3 protein (E.C.3.4.21.90)
    KeywordsVIRUS / alphavirus / bioweapon / VEEV
    Specimen sourceVenezuelan equine encephalitis virus / virus / VEEV
    MethodElectron microscopy (4.8 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsZhang, R. / Hryc, C.F. / 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: Jul 21, 2011 / Release: Aug 24, 2011 / Last modification: Jul 17, 2013

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    Structure visualization

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    • Biological unit as complete icosahedral assembly
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    • Biological unit as icosahedral pentamer
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    • Biological unit as icosahedral 23 hexamer
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    • Deposited structure unit
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    • Simplified surface model + fitted atomic model
    • EMDB-5275
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    Assembly

    Deposited unit
    M: E3 protein
    N: E3 protein
    O: E3 protein
    P: E3 protein

    26 kDa, 4 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    25,9554
    Polyers25,9554
    Non-polymers00
    Water0

    Omokage search
    #1
    M: E3 protein
    N: E3 protein
    O: E3 protein
    P: E3 protein
    x 60
    complete icosahedral assembly / 1.56 MDa, 240 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,557,274240
    Polyers1,557,274240
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x60
    Download / Omokage search
    #2idetical with deposited unit in distinct coordinate / icosahedral asymmetric unit / Symmetry operations: (point symmetry)x1
    #3
    M: E3 protein
    N: E3 protein
    O: E3 protein
    P: E3 protein
    x 5
    icosahedral pentamer / 130 kDa, 20 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    129,77320
    Polyers129,77320
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    M: E3 protein
    N: E3 protein
    O: E3 protein
    P: E3 protein
    x 6
    icosahedral 23 hexamer / 156 kDa, 24 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    155,72724
    Polyers155,72724
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x6
    PAUidetical with deposited unit in distinct coordinate / icosahedral asymmetric unit, std point frame / Symmetry operations: (transform to point frame)x1

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    Components

    #1polypeptide(L) / E3 protein / Spike glycoprotein E3 / Fragment: UNP residues 276-334 / Source: Venezuelan equine encephalitis virus (gene. exp.) / References: UniProt: P05674

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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    Sample preparation

    Assembly of specimenName: Venezuelan Equine Encephalitis Virus TC-83 Strain / Aggregation state: PARTICLE
    Details: The virus contains 240 copies of E1, E2, E3 and capsid proteins
    ComponentName: Venezuelan Equine Encephalitis Virus TC83 strain E3 protein that is cleaved from p62 protein
    Details of the virusEmpty: NO / Enveloped: YES / Virus host category: VERTEBRATES / Virus host growth cell: Baby Hamster Kidney cells / Virus host species: Equus / Virus isolate: STRAIN / Virus type: VIRION
    Buffer solutionName: TEN buffer
    Sample preparationpH: 7.4
    Specimen supportDetails: two of the eight grids used for imaging contained continuous carbon film underneath the samples
    VitrificationInstrument: Vitrobot (FEI Inc) / Cryogen name: ETHANE / Temp: 89.34 K / Humidity: 100 / Details: vitrification carried out in Chiu lab, Houston, TX
    Method: 2 blots, each blot 2 second before plunging, offset = 0

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    Electron microscopy imaging

    MicroscopyMicroscope model: JEOL 3200FSC / Date: Apr 9, 2008 / Details: omega energy filter
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 100000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 400 nm / Cs: 4.3 mm
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Energy filter: Omega Filter
    Specimen holderSpecimen holder model: JEM3200FSC CRYOHOLDER / Specimen holder type: Eucentric / Temperature: 96 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: Gatan 4kx4k CCD Camera
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: CHIMERA
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: projection matching / Software: EMAN / Resolution: 4.8 A / Number of particles: 37000 / Nominal pixel size: 1.07 A/pix
    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).
    Number of class averages: 3328
    Atomic model buildingMethod: rigid-body fitting / Software name: CHIMERA
    Details: The E3 homology model was not further refined against the cryo-EM density map due to its less-resolved quality
    Ref space: REAL
    Number of atoms included #LASTProtein: 1800 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1800

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