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    - EMDB-5006: Structure of immature Dengue virus at low pH -

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    Basic information

    Entry
    Database: EMDB / ID: 5006
    TitleStructure of immature Dengue virus at low pH
    KeywordsDengue virus / maturation
    Sampleimmature Dengue virus
    SourceDengue virus / virus / Dengue
    Map dataimmature Dengue virus particle at pH 6
    Methodsingle particle (icosahedral) reconstruction, at 25 A resolution
    AuthorsYu I / Zhang W / Holdaway HA / Li L / Kostyuchenko VA / Chipman PR / Kuhn RJ / Rossmann MG / Chen J
    CitationScience, 2008, 319, 1834-1837

    Science, 2008, 319, 1834-1837 StrPapers
    Structure of the immature dengue virus at low pH primes proteolytic maturation.
    I-Mei Yu / Wei Zhang / Heather A Holdaway / Long Li / Victor A Kostyuchenko / Paul R Chipman / Richard J Kuhn / Michael G Rossmann / Jue Chen

    DateDeposition: Feb 26, 2008 / Header (metadata) release: Mar 4, 2008 / Map release: Apr 22, 2009 / Last update: Feb 26, 2008

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.691391199
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 0.691391199
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3c6r
    • Surface level: 0.691391199
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5006.map.gz (map file in CCP4 format, 64772 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)X (Row.)Y (Col.)
    255 pix
    2.74 A/pix
    = 698.7 A
    255 pix
    2.74 A/pix
    = 698.7 A
    255 pix
    2.74 A/pix
    = 698.7 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.74 A
    Density
    Contour Level:1.15, 0.6913912 (movie #1):
    Minimum - Maximum-2.09156 - 4.29908
    Average (Standard dev.)1.20983e-07 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderYXZ
    Dimensions255255255
    Origin-127-127-127
    Limit127127127
    Spacing255255255
    CellA=B=C: 698.7 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.742.742.74
    M x/y/z255255255
    origin x/y/z0.0000.0000.000
    length x/y/z698.700698.700698.700
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-127-127-127
    NX/NY/NZ255255255
    MAP C/R/S213
    start NC/NR/NS-127-127-127
    NC/NR/NS255255255
    D min/max/mean-2.0924.2990.000

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    Supplemental data

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    Sample components

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    Entire immature Dengue virus

    EntireName: immature Dengue virus / Number of components: 1

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    Component #1: virus, Dengue virus

    VirusName: Dengue virus / a.k.a: Dengue / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
    SpeciesSpecies: Dengue virus / virus / Dengue
    Source (natural)Host category: VERTEBRATES

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: The virus was mixed in NTE buffer (10 mM Tris, 120 mM NaCl, and 1 mM EDTA at pH 8) with 50 mM MES, 120 mM NaCl at pH 5.6 to yield a final pH of 6
    pH: 6
    Support film400 mesh copper grid
    VitrificationInstrument: NONE / 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.

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 51040 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400 - 2900 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: 14 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12 / OD range: 1

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 231 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: Fourier-Bessel Method / Euler angles: theta:69-90 degrees phi:(-31)-31 degrees / Software: EM3DR / CTF correction: each particle / Resolution: 25 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: EMfit / Refinement protocol: rigid body / Target criteria: Density match / Refinement space: REAL / Details: Protocol: Rigid Body
    Input PDB model: 3c5x
    Output model

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