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    Yorodumi
    - EMDB-2141: 6A Electron cryomicroscopy structure of immature Dengue virus ser... -

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    Basic information

    Entry
    Database: EMDB / ID: 2141
    Title6A Electron cryomicroscopy structure of immature Dengue virus serotype 1
    Keywordsflavivirus / dengue virus serotype 1 / immature / e protein / prM protein / capsid protein
    SampleImmature Dengue virus serotype 1
    SourceDengue virus 1 / virus
    Map dataimmature Dengue virus 1
    Methodsingle particle (icosahedral) reconstruction, at 6 A resolution
    AuthorsKostyuchenko VA / Zhang Q / Tan LC / Ng TS / Lok SM
    CitationJ. Virol., 2013, 87, 7700-7707

    J. Virol., 2013, 87, 7700-7707 StrPapers
    Immature and mature dengue serotype 1 virus structures provide insight into the maturation process.
    Victor A Kostyuchenko / Qian Zhang / Joanne L Tan / Thiam-Seng Ng / Shee-Mei Lok

    DateDeposition: Jun 25, 2012 / Header (metadata) release: Jul 9, 2012 / Map release: Jun 5, 2013 / Last update: Jun 25, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 2.5
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 2.5
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-4b03
    • Surface level: 2.5
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_2141.map.gz (map file in CCP4 format, 843751 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    600 pix
    1.2 A/pix
    = 720. A
    600 pix
    1.2 A/pix
    = 720. A
    600 pix
    1.2 A/pix
    = 720. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.2 A
    Density
    Contour Level:2.5 (by author), 2.5 (movie #1):
    Minimum - Maximum-11.73692226 - 8.14927101
    Average (Standard dev.)-0.03639847 (0.68797463)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions600600600
    Origin-300-300-300
    Limit299299299
    Spacing600600600
    CellA=B=C: 720 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.21.21.2
    M x/y/z600600600
    origin x/y/z0.0000.0000.000
    length x/y/z720.000720.000720.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-32-32-32
    NX/NY/NZ646464
    MAP C/R/S123
    start NC/NR/NS-300-300-300
    NC/NR/NS600600600
    D min/max/mean-11.7378.149-0.036

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    Supplemental data

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    Sample components

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    Entire Immature Dengue virus serotype 1

    EntireName: Immature Dengue virus serotype 1 / Number of components: 1
    MassTheoretical: 14.5 MDa / Experimental: 14.5 MDa
    Measured by: estimation based on components' amino acid sequences

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    Component #1: virus, Dengue virus 1

    VirusName: Dengue virus 1 / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
    MassTheoretical: 14.5 MDa / Experimental: 14.5 MDa
    SpeciesSpecies: Dengue virus 1 / virus / Strain: PVP159 (DEN1/SG/07K3640DK1/2008)
    Source (natural)Host Species: Aedes aegypti / arthropod / / Host category: INVERTEBRATES
    Shell #1Name of element: E / Diameter: 600 A / T number(triangulation number): 1

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionpH: 7.5
    Support filmthin carbon film on lacey carbon support, copper grid, plasma cleaned and glow discharged
    VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Method: blot 1 second before plunging

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    Electron microscopy imaging

    ImagingMicroscope: FEI TITAN KRIOS / Date: Apr 11, 2012
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 17.7 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 75000 X (nominal), 75000 X (calibrated)
    Astigmatism: Astigmatism was corrected at 250,000 magnification
    Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3500 nm / Energy filter: FEI
    Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 100 K ( 99 - 101 K)
    CameraDetector: GENERIC GATAN (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 838 / Bit depth: 16 / Details: CCD data

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 7169 / Details: particles were manually selected / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: MPSA / Software: GPU-adapted, EMAN1
    CTF correction: Wiener filter weighting each particle during 3D reconstruction
    Resolution: 6 A / Resolution method: FSC 0.143

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    Atomic model buiding

    Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: rigid body. Fit in map feature in Chimera, whole structure was fitted as a rigid body with no apparent need to fit domains separately
    Input PDB model: 3c6e
    Chain ID: A, C
    Output model

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