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    - EMDB-1467: Human Parvovirus B19 (empty wildtype particle) -

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    Basic information

    Entry
    Database: EMDB / ID: 1467
    TitleHuman Parvovirus B19 (empty wildtype particle)
    Keywordsicosahedral / empty viral particle / B19
    SampleHuman Parvovirus B19 (empty wildtype particle)
    SourceHuman parvovirus B19 / virus
    Map dataHuman Parvovirus B19 (eB19, empty wildtype particle)
    Methodsingle particle (icosahedral) reconstruction, at 11.3 A resolution
    AuthorsKaufmann B / Chipman PR / Modrow S / Rossmann MG
    CitationJ. Virol., 2008, 82, 7306-7312

    J. Virol., 2008, 82, 7306-7312 StrPapers
    Visualization of the externalized VP2 N termini of infectious human parvovirus B19.
    Bärbel Kaufmann / Paul R Chipman / Victor A Kostyuchenko / Susanne Modrow / Michael G Rossmann

    DateDeposition: Feb 5, 2008 / Header (metadata) release: Feb 7, 2008 / Map release: Mar 31, 2009 / Last update: Feb 5, 2008

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 18
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 18
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1467.map.gz (map file in CCP4 format, 5344 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)X (Row.)Y (Col.)
    111 pix
    2.82 A/pix
    = 312.63 A
    111 pix
    2.82 A/pix
    = 312.63 A
    111 pix
    2.82 A/pix
    = 312.63 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.81649 A
    Density
    Contour Level:11, 18 (movie #1):
    Minimum - Maximum-10.31 - 34.561
    Average (Standard dev.)2.24292 (8.7631)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderYXZ
    Dimensions111111111
    Origin-55-55-55
    Limit555555
    Spacing111111111
    CellA=B=C: 312.63 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.81648648648652.81648648648652.8164864864865
    M x/y/z111111111
    origin x/y/z0.0000.0000.000
    length x/y/z312.630312.630312.630
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-55-55-55
    NX/NY/NZ111111111
    MAP C/R/S213
    start NC/NR/NS-55-55-55
    NC/NR/NS111111111
    D min/max/mean-10.31034.5612.243

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    Supplemental data

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    Sample components

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    Entire Human Parvovirus B19 (empty wildtype particle)

    EntireName: Human Parvovirus B19 (empty wildtype particle)
    Details: icosahedral, empty viral particle, non-enveloped protein shell
    Number of components: 1
    Oligomeric State: 60 VP subunits form icosahedral protein shell
    MassTheoretical: 3.6 MDa

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    Component #1: virus, Human parvovirus B19

    VirusName: Human parvovirus B19 / a.k.a: Human Parvovirus B19 / Class: OTHER
    Details: empty wildtype particles purified from human plasma, no ssDNA genome encapsidated
    Empty: Yes / Enveloped: No / Isolate: SPECIES
    MassTheoretical: 3.6 MDa
    SpeciesSpecies: Human parvovirus B19 / 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 solutionSpecimen conc.: 1 mg/ml / Buffer solution: 25mM Tris-HCl / pH: 7.5
    Support film400 mesh copper
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
    Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.
    Details: Vitrification instrument: guillotine-style plunge freezing device

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM300FEG/T / Details: low dose
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 22 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 45000 X (nominal), 47000 X (calibrated) / Astigmatism: live FFT at 200K / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1250 - 3660 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 98 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 31 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Details: manual particle selection / Number of projections: 1959 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: model-based approach using Fourier methods / Software: EMPFT, POR, P3DR / CTF correction: each particle
    Details: final map includes data to 10.5 Ang resolution (fsc 0.3 cut-off), magnification of final map standardized to a map calculated from B19 VP2 VLP model coordinates (PDB accession no 1S58) resulting in final pixel separation of 2.8165Ang
    Resolution: 11.3 A / Resolution method: FSC 0.5

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