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    Yorodumi
    - EMDB-5414: CryoEM map of the immature human astrovirus HAstV-8 -

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    Basic information

    Entry
    Database: EMDB / ID: 5414
    TitleCryoEM map of the immature human astrovirus HAstV-8
    KeywordsT=3 virus
    Sampleimmature human astrovirus HAstV-8
    SourceHuman astrovirus / virus
    Map datareconstruction of immature human astrovirus HAstV-8
    Methodsingle particle (icosahedral) reconstruction, at 25 A resolution
    AuthorsDryden KA / Tihova M / Nowotny N / Matsui SM / Mendez E / Yeager M
    CitationJ. Mol. Biol., 2012, 422, 650-658

    J. Mol. Biol., 2012, 422, 650-658 StrPapers
    Immature and mature human astrovirus: structure, conformational changes, and similarities to hepatitis E virus.
    Kelly A Dryden / Mariana Tihova / Norbert Nowotny / Suzanne M Matsui / Ernesto Mendez / Mark Yeager

    DateDeposition: Apr 24, 2012 / Header (metadata) release: Jun 28, 2012 / Map release: Jun 28, 2012 / Last update: Apr 24, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.85
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 0.85
    • Imaged by UCSF CHIMERA
    • Download
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5414.map.gz (map file in CCP4 format, 154892 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    341 pix
    1.56 A/pix
    = 531.96 A
    341 pix
    1.56 A/pix
    = 531.96 A
    341 pix
    1.56 A/pix
    = 531.96 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.56 A
    Density
    Contour Level:0.85 (by author), 0.85 (movie #1):
    Minimum - Maximum-4.179986 - 3.50760221
    Average (Standard dev.)0.15266505 (0.67520535)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions341341341
    Origin-170-170-170
    Limit170170170
    Spacing341341341
    CellA=B=C: 531.95996 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.561.561.56
    M x/y/z341341341
    origin x/y/z0.0000.0000.000
    length x/y/z531.960531.960531.960
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-170-170-170
    NC/NR/NS341341341
    D min/max/mean-4.1803.5080.153

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    Supplemental data

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    Sample components

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    Entire immature human astrovirus HAstV-8

    EntireName: immature human astrovirus HAstV-8 / Number of components: 1

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    Component #1: virus, Human astrovirus

    VirusName: Human astrovirus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
    SpeciesSpecies: Human astrovirus / virus
    Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 50mM Tris-HCl, pH 7.4, 100mM NaCl, 10mM EDTA
    Support filmglow discharged with amylamine
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: watch drop spread on filter paper before plunging

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM120T / Date: Dec 22, 2003
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
    LensMagnification: 45000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1450 - 1850 nm
    Specimen HolderModel: GATAN LIQUID NITROGEN
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 7 / Scanner: ZEISS SCAI / Sampling size: 7 microns

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction
    Details: Particles were boxed with X3D and processed with Auto3dem
    Number of projections: 451 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: polar Fourier transform / Software: Auto3dem / Resolution: 25 A / Resolution method: FSC 0.5

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