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    - PDB-1na4: The structure of immature Yellow Fever virus particle -

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    Basic information

    Entry
    Database: PDB / ID: 1na4
    TitleThe structure of immature Yellow Fever virus particle
    Descriptormajor envelope protein E
    KeywordsVirus / flavivirus / flaviviridae / yellow fever immature virus / prM particle / Icosahedral virus
    Specimen sourceYellow fever virus / virus
    MethodElectron microscopy (Single particle / Vitreous ice (cryo EM))
    AuthorsZhang, Y. / Corver, J. / Chipman, P.R. / Lenches, E. / Zhang, W. / Pletnev, S.V. / Sedlak, D. / Baker, T.S. / Strauss, J.H. / Kuhn, R.J. / Rossmann, M.G.
    CitationEMBO J., 2003, 22, 2604-2613

    EMBO J., 2003, 22, 2604-2613 StrPapers
    Structures of immature flavivirus particles.
    Ying Zhang / Jeroen Corver / Paul R Chipman / Wei Zhang / Sergei V Pletnev / Dagmar Sedlak / Timothy S Baker / James H Strauss / Richard J Kuhn / Michael G Rossmann

    DateDeposition: Nov 26, 2002 / Release: Dec 9, 2003 / Last modification: Feb 24, 2009

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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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    Assembly

    Deposited unit
    A: major envelope protein E
    B: major envelope protein E
    C: major envelope protein E

    130 kDa, 3 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    129,6953
    Polyers129,6953
    Non-polymers00
    Water0

    Omokage search
    #1
    A: major envelope protein E
    B: major envelope protein E
    C: major envelope protein E
    x 60
    complete icosahedral assembly / 7.78 MDa, 180 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    7,781,683180
    Polyers7,781,683180
    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: major envelope protein E
    B: major envelope protein E
    C: major envelope protein E
    x 5
    icosahedral pentamer / 648 kDa, 15 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    648,47415
    Polyers648,47415
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: major envelope protein E
    B: major envelope protein E
    C: major envelope protein E
    x 6
    icosahedral 23 hexamer / 778 kDa, 18 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    778,16818
    Polyers778,16818
    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) / major envelope protein E / Source: Yellow fever virus (gene. exp.) / References: UniProt: P14336

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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: Yellow fever immature virus / Aggregation state: PARTICLE
    Details: The samples were produced by adding ammonium chloride to the medium in the late infection stage.

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    Processing

    Image selectionSoftware name: EMFIT
    EM single particle entitySymmetry type: ICOSAHEDRAL
    Atomic model buildingSoftware name: EMFIT / Ref space: REAL
    Number of atoms included #LASTProtein: 1185 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1185

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