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    - PDB-3j0f: Sindbis virion -

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    Basic information

    Entry
    Database: PDB / ID: 3j0f
    TitleSindbis virion
    DescriptorCapsid protein (E.C.3.4.21.90)
    E1 envelope glycoprotein
    E2 envelope glycoprotein
    KeywordsVIRUS / alphavirus / virus assembly / glycoprotein
    Specimen sourceSindbis virus / virus / SINV
    MethodElectron microscopy (7 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsTang, J. / Jose, J. / Zhang, W. / Chipman, P. / Kuhn, R.J. / Baker, T.S.
    CitationJ. Mol. Biol., 2011, 414, 442-459

    J. Mol. Biol., 2011, 414, 442-459 StrPapers
    Molecular links between the E2 envelope glycoprotein and nucleocapsid core in Sindbis virus.
    Jinghua Tang / Joyce Jose / Paul Chipman / Wei Zhang / Richard J Kuhn / Timothy S Baker

    DateDeposition: Jul 8, 2011 / Release: Oct 12, 2011 / Last modification: May 30, 2012

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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-5251
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    Assembly

    Deposited unit
    A: Capsid protein
    B: Capsid protein
    C: Capsid protein
    D: Capsid protein
    E: E1 envelope glycoprotein
    F: E1 envelope glycoprotein
    G: E1 envelope glycoprotein
    H: E1 envelope glycoprotein
    I: E2 envelope glycoprotein
    J: E2 envelope glycoprotein
    K: E2 envelope glycoprotein
    L: E2 envelope glycoprotein

    495 kDa, 12 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    495,24212
    Polyers495,24212
    Non-polymers00
    Water0

    Omokage search
    #1
    A: Capsid protein
    B: Capsid protein
    C: Capsid protein
    D: Capsid protein
    E: E1 envelope glycoprotein
    F: E1 envelope glycoprotein
    G: E1 envelope glycoprotein
    H: E1 envelope glycoprotein
    I: E2 envelope glycoprotein
    J: E2 envelope glycoprotein
    K: E2 envelope glycoprotein
    L: E2 envelope glycoprotein
    x 60
    complete icosahedral assembly / 29.7 MDa, 720 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    29,714,545720
    Polyers29,714,545720
    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
    A: Capsid protein
    B: Capsid protein
    C: Capsid protein
    D: Capsid protein
    E: E1 envelope glycoprotein
    F: E1 envelope glycoprotein
    G: E1 envelope glycoprotein
    H: E1 envelope glycoprotein
    I: E2 envelope glycoprotein
    J: E2 envelope glycoprotein
    K: E2 envelope glycoprotein
    L: E2 envelope glycoprotein
    x 5
    icosahedral pentamer / 2.48 MDa, 60 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    2,476,21260
    Polyers2,476,21260
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: Capsid protein
    B: Capsid protein
    C: Capsid protein
    D: Capsid protein
    E: E1 envelope glycoprotein
    F: E1 envelope glycoprotein
    G: E1 envelope glycoprotein
    H: E1 envelope glycoprotein
    I: E2 envelope glycoprotein
    J: E2 envelope glycoprotein
    K: E2 envelope glycoprotein
    L: E2 envelope glycoprotein
    x 6
    icosahedral 23 hexamer / 2.97 MDa, 72 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    2,971,45472
    Polyers2,971,45472
    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) / Capsid protein / Coat protein, C / Fragment: UNP residues 1-264 / Source: Sindbis virus (gene. exp.) / References: UniProt: P03316, EC: 3.4.21.90
    #2polypeptide(L) / E1 envelope glycoprotein / Spike glycoprotein E1 / Fragment: UNP residues 807-1245 / Source: Sindbis virus (gene. exp.) / References: UniProt: P03316
    #3polypeptide(L) / E2 envelope glycoprotein / Spike glycoprotein E2 / Fragment: UNP residues 329-751 / Source: Sindbis virus (gene. exp.) / References: UniProt: P03316

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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: sindbis virion / Aggregation state: PARTICLE / Number of components: 60
    ComponentName: alphavirus / Type: VIRUS
    Details of the virusEmpty: NO / Enveloped: YES / Virus host category: VERTEBRATES / Virus host species: Homo sapiens / Virus isolate: STRAIN / Virus type: VIRION
    VitrificationCryogen name: ETHANE

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    Electron microscopy imaging

    EM imagingCamera length: 0 mm
    MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Dec 12, 2001
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD
    Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: eucentric / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: Kodak SO163 film
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionResolution: 7 A
    Atomic model buildingRef space: REAL
    Number of atoms included #LASTProtein: 4064 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 4064

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