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EMDB-5428: Cryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) c... - Yorodumi

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    - EMDB-5428: Cryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) c... -

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    Basic information

    Entry
    Database: EMDB / ID: 5428
    TitleCryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
    KeywordsTime-resolved / T=4 / quasi-equivalence / maturation
    SampleNudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
    SourceNudaurelia capensis omega virus / virus / NwV (N omega V)
    Map dataReconstruction of Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
    Methodsingle particle (icosahedral) reconstruction, at 8.3 A resolution
    AuthorsMatsui T / Lander GC / Khayat R / Johnson JE
    CitationProc. Natl. Acad. Sci. U.S.A., 2010, 107, 14111-14115

    Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 14111-14115 StrPapers
    Subunits fold at position-dependent rates during maturation of a eukaryotic RNA virus.
    Tsutomu Matsui / Gabriel C Lander / Reza Khayat / John E Johnson

    DateDeposition: May 29, 2012 / Header (metadata) release: Jun 4, 2012 / Map release: Jun 4, 2012 / Last update: May 29, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_5428.map.gz (map file in CCP4 format, 31251 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    200 pix
    2.77 A/pix
    = 553.6 A
    200 pix
    2.77 A/pix
    = 553.6 A
    200 pix
    2.77 A/pix
    = 553.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.768 A
    Density
    Contour Level:1 (by author), 1 (movie #1):
    Minimum - Maximum-4.57011175 - 7.01301813
    Average (Standard dev.)0E-8 (0.99999994)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions200200200
    Origin-100-100-100
    Limit999999
    Spacing200200200
    CellA=B=C: 553.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.7682.7682.768
    M x/y/z200200200
    origin x/y/z0.0000.0000.000
    length x/y/z553.600553.600553.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-150-1500
    NX/NY/NZ301301151
    MAP C/R/S123
    start NC/NR/NS-100-100-100
    NC/NR/NS200200200
    D min/max/mean-4.5707.013-0.000

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    Supplemental data

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    Sample components

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    Entire Nudaurelia capensis omega virus (NwV) capsid at 4hr time point fo...

    EntireName: Nudaurelia capensis omega virus (NwV) capsid at 4hr time point following maturation initiation
    Number of components: 1 / Oligomeric State: Icosahedral virus

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    Component #1: virus, Nudaurelia capensis omega virus

    VirusName: Nudaurelia capensis omega virus / a.k.a: NwV (N omega V) / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / Isolate: STRAIN
    SpeciesSpecies: Nudaurelia capensis omega virus / virus / NwV (N omega V)
    Source (natural)Host Species: Lepidoptera / Host category: INVERTEBRATES

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 10 mg/ml / Buffer solution: 100mM NaOAc, 250mM NaCl / pH: 5
    VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 % / Method: Blot for 5sec before plunging

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Feb 13, 2008
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 16.5 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 80000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm
    Specimen HolderModel: GATAN LIQUID NITROGEN

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 23392 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: Projection matching / Software: EMAN / CTF correction: Each image
    Details: Data processing was performed using the Appion pipeline.
    Resolution: 8.3 A / Resolution method: FSC 0.5

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