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    Yorodumi
    - EMDB-1661: The three-dimensional structure of a hepatitis C virus p7 ion cha... -

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    Basic information

    Entry
    Database: EMDB / ID: 1661
    TitleThe three-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy
    SampleHCV p7 hexamer, JFH-1 strain, genotype 2a
    SourceHepatitis C virus / virus
    Map dataTop view of the EM density map of the HCV p7 channel
    Methodsingle particle reconstruction, at 16 A resolution
    AuthorsLuik P / Chew C / Aittoniemi J / Chang J / Wentworth P / Dwek RA / Biggin PC / Venien-Bryan C / Zitzmann N
    CitationProc. Natl. Acad. Sci. U.S.A., 2009, 106, 12712-12716

    Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 12712-12716 StrPapers
    The 3-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy.
    Philipp Luik / Chee Chew / Jussi Aittoniemi / Jason Chang / Paul Wentworth / Raymond A Dwek / Philip C Biggin / Catherine Vénien-Bryan / Nicole Zitzmann

    DateDeposition: Nov 4, 2009 / Header (metadata) release: Nov 17, 2009 / Map release: Nov 17, 2009 / Last update: Nov 4, 2009

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.035
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.035
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1661.map.gz (map file in CCP4 format, 1025 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    64 pix
    2.77 A/pix
    = 177.28 A
    64 pix
    2.77 A/pix
    = 177.28 A
    64 pix
    2.77 A/pix
    = 177.28 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.77 A
    Density
    Contour Level:0.035 (by author), 0.035 (movie #1):
    Minimum - Maximum-0.0164729 - 0.0843588
    Average (Standard dev.)0.00149795 (0.00843059)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions646464
    Origin-32-32-32
    Limit313131
    Spacing646464
    CellA=B=C: 177.28 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.772.772.77
    M x/y/z646464
    origin x/y/z0.0000.0000.000
    length x/y/z177.280177.280177.280
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-147-147-147
    NX/NY/NZ294294294
    MAP C/R/S123
    start NC/NR/NS-32-32-32
    NC/NR/NS646464
    D min/max/mean-0.0160.0840.001

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    Supplemental data

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    Sample components

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    Entire HCV p7 hexamer, JFH-1 strain, genotype 2a

    EntireName: HCV p7 hexamer, JFH-1 strain, genotype 2a / Number of components: 1 / Oligomeric State: Hexameric

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    Component #1: protein, p7

    ProteinName: p7 / a.k.a: p7 / Details: p7 solubilzed with DHPC / Recombinant expression: No
    SourceSpecies: Hepatitis C virus / virus

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 100 mM NaCl, 50 mM DHPC, 25 mM Hepes, pH 7.0
    pH: 7
    Staining2% (w/v) phosphotungstic acid (PTA)
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM120T
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: SPOT SCAN
    LensImaging mode: BRIGHT FIELD
    Specimen HolderHolder: Eucentric / Model: PHILIPS ROTATION HOLDER
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: NIKON SUPER COOLSCAN 9000

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    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: C6 (6 fold cyclic)
    3D reconstructionResolution: 16 A / Resolution method: FSC 0.5

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