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    Yorodumi
    - EMDB-5413: CryoEM map of the mature astrovirus (HAstV-1) -

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    Basic information

    Entry
    Database: EMDB / ID: 5413
    TitleCryoEM map of the mature astrovirus (HAstV-1)
    KeywordsT=3 virus
    Samplemature human astrovirus HAstV-1
    SourceHuman astrovirus / virus
    Map dataReconstruction of mature human astrovirus HAstV-1
    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: 55
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 55
    • Imaged by UCSF CHIMERA
    • Download
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5413.map.gz (map file in CCP4 format, 61772 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    251 pix
    2 A/pix
    = 502. A
    251 pix
    2 A/pix
    = 502. A
    251 pix
    2 A/pix
    = 502. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2 A
    Density
    Contour Level:55 (by author), 55 (movie #1):
    Minimum - Maximum-189.82514954 - 244.88218689
    Average (Standard dev.)6.81235361 (36.43178558)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions251251251
    Origin-125-125-125
    Limit125125125
    Spacing251251251
    CellA=B=C: 502 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z222
    M x/y/z251251251
    origin x/y/z0.0000.0000.000
    length x/y/z502.000502.000502.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-125-125-125
    NC/NR/NS251251251
    D min/max/mean-189.825244.8826.812

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    Supplemental data

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    Sample components

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    Entire mature human astrovirus HAstV-1

    EntireName: mature human astrovirus HAstV-1 / 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 8, 100mM NaCl, 10mM MgCl2, 10mM CaCl2
    Support filmholey carbon, glow 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: Sep 22, 1997
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
    LensMagnification: 35000 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: 6 / Scanner: ZEISS SCAI / Sampling size: 7 microns

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction
    Details: Particles were selected with X3D, and processed with Auto3dem.
    Number of projections: 397 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: polar Fourier transform / Software: Auto3dem / Resolution: 25 A / Resolution method: FSC 0.5

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