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    Yorodumi
    - EMDB-2073: Structure of the dengue virus glycoprotein non-structural protein... -

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    Basic information

    Entry
    Database: EMDB / ID: 2073
    TitleStructure of the dengue virus glycoprotein non-structural protein 1 by electron microscopy and single-particle analysis
    KeywordsFlavivirus / Dengue / NS1 / glycoprotein
    SampleSecreted form of DENV-2 NS1
    SourceDengue virus 2 / virus
    Map data3D reconstruction of recombinant DENV-2 sNS1 protein
    Methodsingle particle reconstruction, at 23 A resolution
    AuthorsMuller DA / Landsberg MJ / Bletchly C / Rothnagel R / Waddington L / Hankamer B / Young PR
    CitationJ. Gen. Virol., 2012, 93, 771-779

    J. Gen. Virol., 2012, 93, 771-779 StrPapers
    Structure of the dengue virus glycoprotein non-structural protein 1 by electron microscopy and single-particle analysis.
    David A Muller / Michael J Landsberg / Cheryl Bletchly / Rosalba Rothnagel / Lynne Waddington / Ben Hankamer / Paul R Young

    DateDeposition: Apr 13, 2012 / Header (metadata) release: Apr 17, 2012 / Map release: Apr 17, 2012 / Last update: Apr 13, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.04
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 1.04
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_2073.map.gz (map file in CCP4 format, 4922 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    108 pix
    1.86 A/pix
    = 200.88 A
    108 pix
    1.86 A/pix
    = 200.88 A
    108 pix
    1.86 A/pix
    = 200.88 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.86 A
    Density
    Contour Level:1.04 (by author), 1.04 (movie #1):
    Minimum - Maximum-3.1992631 - 6.28529167
    Average (Standard dev.)0.02490416 (0.49955314)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions108108108
    Origin-135-135-135
    Limit-28-28-28
    Spacing108108108
    CellA=B=C: 200.88 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.861.861.86
    M x/y/z108108108
    origin x/y/z0.0000.0000.000
    length x/y/z200.880200.880200.880
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ000
    NX/NY/NZ128128168
    MAP C/R/S123
    start NC/NR/NS-135-135-135
    NC/NR/NS108108108
    D min/max/mean-3.1996.2850.025

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    Supplemental data

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    Sample components

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    Entire Secreted form of DENV-2 NS1

    EntireName: Secreted form of DENV-2 NS1 / Details: Monodisperse sample as assessed by SEC / Number of components: 1 / Oligomeric State: Homohexamer
    MassTheoretical: 246 kDa

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    Component #1: protein, Non structural protein 1

    ProteinName: Non structural protein 1 / a.k.a: NS1 / Oligomeric Details: Hexamer / Recombinant expression: Yes / Number of Copies: 6
    MassTheoretical: 41 kDa
    SourceSpecies: Dengue virus 2 / virus
    Source (engineered)Expression System: Spodoptera / arthropod / Vector: pFastBac
    Source (natural)Location in cell: Secreted
    External referencesInterPro: InterPro: 001157

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.1 mg/ml / Buffer solution: 20 mM Tris, 300 mM NaCl / pH: 8
    Support film400 mesh copper grid with thin carbon support, glow discharged
    StainingGrids with adsorbed protein washed with an aqueous solution of 2% (w/v) uranyl acetate for 30 seconds.
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 12 / Date: Sep 17, 2003
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 60 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 68000 X (nominal)
    Astigmatism: objective lens astigmatism was corrected at 93,000 times magnification
    Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 200 - 1000 nm
    Specimen HolderHolder: FEI single tilt room temperature / Model: SIDE ENTRY, EUCENTRIC / Temperature: 295 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 40 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 174 / Number of projections: 3523
    Details: Particles selected semi-automatically using the SWARM-PS software
    Applied symmetry: C3 (3 fold cyclic)
    3D reconstructionAlgorithm: Angular reconstitution / Software: IMAGIC, EMAN, XMIPP
    Details: An exhaustive evaluation of point symmetry was performed as described in the associated manuscript
    Resolution: 23 A / Resolution method: FSC 0.5

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