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    Yorodumi
    - EMDB-1986: CryoEM reconstruction of the Marburg virus nucleocapsid. -

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    Basic information

    Entry
    Database: EMDB / ID: 1986
    TitleCryoEM reconstruction of the Marburg virus nucleocapsid.
    KeywordsMarburg / virus / nucleocapsid / Nucleoprotein / VP24 / VP35
    SampleMarburg virus nucleocapsid
    SourceMarburg marburgvirus / virus / Marburg virus
    Map dataThis is a map of the Marburg virus nucleocapsid within virions.
    Methodhelical reconstruction, at 25 A resolution
    AuthorsBharat TAM / Riches JD / Kolesnikova L / Welsch S / Kraehling V / Davey N / Parsy ML / Becker S / Briggs JAG
    CitationPLoS Biol., 2011, 9, e1001196-e1001196

    PLoS Biol., 2011, 9, e1001196-e1001196 StrPapers
    Cryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells.
    Tanmay A M Bharat / James D Riches / Larissa Kolesnikova / Sonja Welsch / Verena Krähling / Norman Davey / Marie-Laure Parsy / Stephan Becker / John A G Briggs

    DateDeposition: Nov 11, 2011 / Header (metadata) release: Nov 17, 2011 / Map release: Nov 17, 2011 / Last update: Nov 11, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.00124
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.00124
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1986.map.gz (map file in CCP4 format, 7912 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    90 pix
    4 A/pix
    = 360. A
    150 pix
    4 A/pix
    = 600. A
    150 pix
    4 A/pix
    = 600. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4 A
    Density
    Contour Level:0.00124 (by author), 0.00124 (movie #1):
    Minimum - Maximum-0.00187585 - 0.00387182
    Average (Standard dev.)0.00040353 (0.000906448)
    Details

    EMDB XML:

    Space Group Number0
    Map Geometry
    Axis orderXYZ
    Dimensions15015090
    Origin000
    Limit14914989
    Spacing15015090
    CellA: 600 A / B: 600 A / C: 360 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z444
    M x/y/z15015090
    origin x/y/z-0.000-0.000-0.000
    length x/y/z600.000600.000360.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS15015090
    D min/max/mean-0.0020.0040.000

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    Supplemental data

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    Sample components

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    Entire Marburg virus nucleocapsid

    EntireName: Marburg virus nucleocapsid / Number of components: 1

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    Component #1: virus, Marburg marburgvirus

    VirusName: Marburg marburgvirus / a.k.a: Marburg virus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
    SpeciesSpecies: Marburg marburgvirus / virus / Marburg virus
    Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES

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    Experimental details

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    Sample preparation

    Specimen statefilament
    Helical parametersHand: LEFT HANDED / Delta z: 5 A / Delta phi: 24.3 deg.
    Sample solutionBuffer solution: PBS buffer with 4% PFA.
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: Plunge freezing / Details: Vitrification instrument: Plunge freezer

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM120T
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 37000 X (nominal) / Cs: 6.3 mm / Imaging mode: BRIGHT FIELD / Defocus: 0.6 - 4 nm
    Specimen HolderHolder: Gatan 626 / Model: GATAN LIQUID NITROGEN
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: ZEISS SCAI / Sampling size: 14 microns

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    Image processing

    ProcessingMethod: helical reconstruction
    3D reconstructionAlgorithm: real-space helical / Software: Spider, Bsoft / CTF correction: Phase flip / Resolution: 25 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: Rigid body. 4 monomers from the VSV Nucleoprotein structure were fitted in as a single rigid body without any corrections.
    Input PDB model: 2WYY

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