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    Yorodumi
    - PDB-2xfc: CHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SEMLIKI FOREST... -

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    Basic information

    Entry
    Database: PDB / ID: 2xfc
    TitleCHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SEMLIKI FOREST VIRUS cryo-EM MAP
    DescriptorE1 ENVELOPE GLYCOPROTEIN
    E2 ENVELOPE GLYCOPROTEIN
    KeywordsVIRUS / RECEPTOR BINDING / MEMBRANE FUSION / ICOSAHEDRAL ENVELOPED VIRUS
    Specimen sourceCHIKUNGUNYA VIRUS / virus
    MethodElectron microscopy (9 A resolution / Single particle)
    AuthorsVoss, J.E. / Vaney, M.C. / Duquerroy, S. / Rey, F.A.
    CitationNature, 2010, 468, 709-712

    primary. Nature, 2010, 468, 709-712 StrPapers
    Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography.
    James E Voss / Marie-Christine Vaney / Stéphane Duquerroy / Clemens Vonrhein / Christine Girard-Blanc / Elodie Crublet / Andrew Thompson / Gérard Bricogne / Félix A Rey

    #1. Mol.Cell, 2000, 5, 255- StrPapers
    Cryo-Electron Microscopy Reveals the Functional Organization of an Enveloped Virus, Semliki Forest Virus.
    Mancini, E.J. / Clarke, M. / Gowen, B.E. / Rutten, T. / Fuller, S.D.

    DateDeposition: May 21, 2010 / Release: Nov 24, 2010 / Last modification: Sep 25, 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-1015
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    Assembly

    Deposited unit
    A: E1 ENVELOPE GLYCOPROTEIN
    B: E2 ENVELOPE GLYCOPROTEIN
    D: E1 ENVELOPE GLYCOPROTEIN
    E: E2 ENVELOPE GLYCOPROTEIN
    F: E1 ENVELOPE GLYCOPROTEIN
    G: E2 ENVELOPE GLYCOPROTEIN
    H: E1 ENVELOPE GLYCOPROTEIN
    I: E2 ENVELOPE GLYCOPROTEIN

    379 kDa, 8 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    379,3448
    Polyers379,3448
    Non-polymers00
    Water0

    Omokage search
    #1
    A: E1 ENVELOPE GLYCOPROTEIN
    B: E2 ENVELOPE GLYCOPROTEIN
    D: E1 ENVELOPE GLYCOPROTEIN
    E: E2 ENVELOPE GLYCOPROTEIN
    F: E1 ENVELOPE GLYCOPROTEIN
    G: E2 ENVELOPE GLYCOPROTEIN
    H: E1 ENVELOPE GLYCOPROTEIN
    I: E2 ENVELOPE GLYCOPROTEIN
    x 60
    complete icosahedral assembly / 22.8 MDa, 480 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    22,760,631480
    Polyers22,760,631480
    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: E1 ENVELOPE GLYCOPROTEIN
    B: E2 ENVELOPE GLYCOPROTEIN
    D: E1 ENVELOPE GLYCOPROTEIN
    E: E2 ENVELOPE GLYCOPROTEIN
    F: E1 ENVELOPE GLYCOPROTEIN
    G: E2 ENVELOPE GLYCOPROTEIN
    H: E1 ENVELOPE GLYCOPROTEIN
    I: E2 ENVELOPE GLYCOPROTEIN
    x 5
    icosahedral pentamer / 1.9 MDa, 40 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,896,71940
    Polyers1,896,71940
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: E1 ENVELOPE GLYCOPROTEIN
    B: E2 ENVELOPE GLYCOPROTEIN
    D: E1 ENVELOPE GLYCOPROTEIN
    E: E2 ENVELOPE GLYCOPROTEIN
    F: E1 ENVELOPE GLYCOPROTEIN
    G: E2 ENVELOPE GLYCOPROTEIN
    H: E1 ENVELOPE GLYCOPROTEIN
    I: E2 ENVELOPE GLYCOPROTEIN
    x 6
    icosahedral 23 hexamer / 2.28 MDa, 48 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    2,276,06348
    Polyers2,276,06348
    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) / E1 ENVELOPE GLYCOPROTEIN / Fragment: ECTODOMAIN, RESIDUES 810-1248 / Source: CHIKUNGUNYA VIRUS (gene. exp.) / References: UniProt: Q1H8W5
    #2polypeptide(L) / E2 ENVELOPE GLYCOPROTEIN / Fragment: ECTODOMAIN, RESIDUES 326-748 / Source: CHIKUNGUNYA VIRUS (gene. exp.) / References: UniProt: Q1H8W5

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: SINGLE PARTICLE

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    Sample preparation

    Assembly of specimenAggregation state: PARTICLE
    Specimen supportDetails: OTHER

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    Electron microscopy imaging

    MicroscopyMicroscope model: OTHER
    Electron gunElectron source: OTHER / Accelerating voltage: 100 kV
    Electron lensMode: OTHER
    Radiation wavelengthRelative weight: 1

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    Processing

    3D reconstructionResolution: 9 A
    Details: THE COMPLETE PARTICLE IS GENERATED BY BIOMT MATRICES. THE FIT WAS GENERATED WITH URO IN SINDBIS CRYO-EM MAP EMDB-1015 THAT WAS CORRECTED IN MAGNITUDE BY MULTIPLYING A FACTOR OF 1.038 AND USING PDB ENTRY 3N40
    Least-squares processHighest resolution: 9 A
    Refine hist #LASTHighest resolution: 9 A
    Number of atoms included #LASTProtein: 22420 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 22420

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