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    - EMDB-1418: Binding of a neutralizing antibody to dengue virus alters the arr... -

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    Basic information

    Entry
    Database: EMDB / ID: 1418
    TitleBinding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins
    SampleFab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
    SourceDengue virus 2 / virus / DENV
    Mus musculus / mammal / House mouse /
    Map dataThis is a map of Fab 1A1D-2 complexed with Dengue virus
    Methodsingle particle (icosahedral) reconstruction, at 24 A resolution
    AuthorsLok SM
    CitationNat. Struct. Mol. Biol., 2008, 15, 312-317

    Nat. Struct. Mol. Biol., 2008, 15, 312-317 StrPapers
    Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins.
    Shee-Mei Lok / Victor Kostyuchenko / Grant E Nybakken / Heather A Holdaway / Anthony J Battisti / Soila Sukupolvi-Petty / Dagmar Sedlak / Daved H Fremont / Paul R Chipman / John T Roehrig / Michael S Diamond / Richard J Kuhn / Michael G Rossmann

    DateDeposition: Sep 7, 2007 / Header (metadata) release: Sep 7, 2007 / Map release: Jan 2, 2008 / Last update: Sep 7, 2007

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.98
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 1.98
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-2r6p
    • Surface level: 1.98
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1418.map.gz (map file in CCP4 format, 93313 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    288 pix
    2.74 A/pix
    = 789.12 A
    288 pix
    2.74 A/pix
    = 789.12 A
    288 pix
    2.74 A/pix
    = 789.12 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:1.98, 1.98 (movie #1):
    Minimum - Maximum-4.12769 - 8.46468
    Average (Standard dev.)0.00957931 (0.995975)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions288288288
    Origin-144-144-144
    Limit143143143
    Spacing288288288
    CellA=B=C: 789.12 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.742.742.74
    M x/y/z288288288
    origin x/y/z0.0000.0000.000
    length x/y/z789.120789.120789.120
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-30-30-49
    NX/NY/NZ6060100
    MAP C/R/S123
    start NC/NR/NS-144-144-144
    NC/NR/NS288288288
    D min/max/mean-4.1288.4650.010

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    Supplemental data

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    Sample components

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    Entire Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus

    EntireName: Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
    Oligomeric State: The Fab molecule binds to two of the three E proteins in the icosahedral assymmetric unit
    Number of components: 2

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    Component #1: virus, Dengue virus 2

    VirusName: Dengue virus 2 / a.k.a: DENV / Class: VIRION / Enveloped: Yes / Empty: No / Isolate: SEROTYPE
    SpeciesSpecies: Dengue virus 2 / virus / DENV
    Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES
    Shell #1Name of element: envelope / Diameter: 240 A / T number(triangulation number): 3

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    Component #2: protein, Fab fragment of MAb 1A1D-2

    ProteinName: Fab fragment of MAb 1A1D-2 / a.k.a: 1A1D-2 / Oligomeric Details: heterodimer / Recombinant expression: No / Number of Copies: 2
    MassTheoretical: 50 MDa / Experimental: 50 MDa
    SourceSpecies: Mus musculus / mammal / House mouse /
    Source (natural)Cell: hybridoma

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.6 mg/ml / Buffer solution: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA / pH: 7.6
    Support film400 mesh copper grid
    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 freezeing device

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200T / Date: Mar 21, 2007 / Details: low dose
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 24 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 51040 X (calibrated) / Astigmatism: live FFT / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2270 - 3370 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 98 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionSampling size: 7 microns

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    Image processing

    ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 2885 / Applied symmetry: I (icosahedral)
    3D reconstructionAlgorithm: projection matching / Software: spider,XMIPP / CTF correction: each particle / Resolution: 24 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: EMFIT / Refinement protocol: rigid body / Details: Protocol: Rigid body
    Input PDB model: 1THD
    Chain ID: 2R29
    Output model

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