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    - PDB-3muw: Pseudo-atomic structure of the E2-E1 protein shell in Sindbis virus -

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    Basic information

    Entry
    Database: PDB / ID: 3muw
    TitlePseudo-atomic structure of the E2-E1 protein shell in Sindbis virus
    DescriptorStructural polyprotein (E.C.3.4.21.-)
    KeywordsVIRUS / icosahedral protein shell / icosahedral virus
    Specimen sourceSindbis virus / virus / SINV
    MethodElectron microscopy (9 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsLi, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G.
    CitationNature, 2010, 468, 705-708

    Nature, 2010, 468, 705-708 StrPapers
    Structural changes of envelope proteins during alphavirus fusion.
    Long Li / Joyce Jose / Ye Xiang / Richard J Kuhn / Michael G Rossmann

    DateDeposition: May 3, 2010 / Release: Nov 24, 2010 / Last modification: May 4, 2011

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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-1121
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    Assembly

    Deposited unit
    A: Structural polyprotein
    U: Structural polyprotein
    D: Structural polyprotein
    X: Structural polyprotein
    E: Structural polyprotein
    Y: Structural polyprotein
    F: Structural polyprotein
    Z: Structural polyprotein

    319 kDa, 8 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    319,2858
    Polyers319,2858
    Non-polymers00
    Water0

    Omokage search
    #1
    A: Structural polyprotein
    U: Structural polyprotein
    D: Structural polyprotein
    X: Structural polyprotein
    E: Structural polyprotein
    Y: Structural polyprotein
    F: Structural polyprotein
    Z: Structural polyprotein
    x 60
    complete icosahedral assembly / 19.2 MDa, 480 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    19,157,073480
    Polyers19,157,073480
    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: Structural polyprotein
    U: Structural polyprotein
    D: Structural polyprotein
    X: Structural polyprotein
    E: Structural polyprotein
    Y: Structural polyprotein
    F: Structural polyprotein
    Z: Structural polyprotein
    x 5
    icosahedral pentamer / 1.6 MDa, 40 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,596,42340
    Polyers1,596,42340
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: Structural polyprotein
    U: Structural polyprotein
    D: Structural polyprotein
    X: Structural polyprotein
    E: Structural polyprotein
    Y: Structural polyprotein
    F: Structural polyprotein
    Z: Structural polyprotein
    x 6
    icosahedral 23 hexamer / 1.92 MDa, 48 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,915,70748
    Polyers1,915,70748
    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) / Structural polyprotein / p130, Capsid protein, Coat protein, C, p62, E3/E2, E3 protein, Spike glycoprotein E3, E2 envelope glycoprotein, Spike glycoprotein E2, 6K protein, E1 envelope glycoprotein, Spike glycoprotein E1 / Source: Sindbis virus (gene. exp.) / References: UniProt: P03316, EC: 3.4.21.-
    #2polypeptide(L) / Structural polyprotein / p130, Capsid protein, Coat protein, C, p62, E3/E2, E3 protein, Spike glycoprotein E3, E2 envelope glycoprotein, Spike glycoprotein E2, 6K protein, E1 envelope glycoprotein, Spike glycoprotein E1 / Source: Sindbis virus (gene. exp.) / References: UniProt: P03316, EC: 3.4.21.-

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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 virus / Aggregation state: PARTICLE
    ComponentName: E2-E1 protein shell of Sindbis virus
    Details of the virusVirus host category: VERTEBRATES / Virus host growth cell: BHK cell / Virus host species: homo sapiens / Virus isolate: STRAIN / Virus type: Virion
    Buffer solutionName: TNE buffer
    Sample preparationpH: 7.5 / Sample conc.: 5 mg/ml
    Specimen supportDetails: This grid plus sample was kept at 100 K

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI/PHILIPS CM200T / Date: Jun 21, 2000
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 18 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 X / Calibrated magnification: 39220 X / Nominal defocus max: 2580 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
    Specimen holderTilt 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

    Image selectionSoftware name: EMfit / Number of particles: 7085
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionMethod: model-based common lines / Resolution: 9 A / CTF correction method: CTF correction of each particle.
    Atomic model buildingSoftware name: EMfit / Ref protocol: rigid body / Ref space: REAL / Target criteria: sumf
    Number of atoms included #LASTProtein: 2468 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2468

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