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    Yorodumi
    - EMDB-5325: Molecular structure of soluble trimeric HIV-1 glycoprotein gp140 ... -

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    Basic information

    Entry
    Database: EMDB / ID: 5325
    TitleMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with 17b
    KeywordsHIV/AIDS vaccine / immunogen / HIV glycoprotein structure / gp140 trimer / cryo-electron tomography / sub-tomogram averaging / cryo-electron microscopy
    SampleSOSIP gp140 KNH1144 17b
    SourceHuman immunodeficiency virus 1 / virus
    Map dataMolecular structure of soluble trimeric HIV-1 glycoprotein gp140 KNH1144 with 17b
    Methodsubtomogram averaging, at 20 A resolution
    AuthorsHarris A / Borgnia MJ / Shi D / Bartesaghi A / He H / Pejchal R / Kang YK / Depetris R / Marozsan AJ / Sanders RW / Klasse PJ / Milne JL / Wilson IA / Olson WC / Moore JP / Subramaniam S
    CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 11440-11445

    Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 11440-11445 StrPapers
    Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures.
    Audray Harris / Mario J Borgnia / Dan Shi / Alberto Bartesaghi / Haifeng He / Robert Pejchal / Yun Kenneth Kang / Rafael Depetris / Andre J Marozsan / Rogier W Sanders / Per Johan Klasse / Jacqueline L S Milne / Ian A Wilson / William C Olson / John P Moore / Sriram Subramaniam

    DateDeposition: Jul 11, 2011 / Header (metadata) release: May 31, 2012 / Map release: May 31, 2012 / Last update: Jul 11, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 2
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 2
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_5325.map.gz (map file in CCP4 format, 3908 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    100 pix
    4.1 A/pix
    = 410. A
    100 pix
    4.1 A/pix
    = 410. A
    100 pix
    4.1 A/pix
    = 410. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.1 A
    Density
    Contour Level:2 (by author), 2 (movie #1):
    Minimum - Maximum-6.37717438 - 8.50566101
    Average (Standard dev.)-0.00243358 (0.6463089)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions100100100
    Origin000
    Limit999999
    Spacing100100100
    CellA=B=C: 410 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z4.14.14.1
    M x/y/z100100100
    origin x/y/z0.0000.0000.000
    length x/y/z410.000410.000410.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS100100100
    D min/max/mean-6.3778.506-0.002

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    Supplemental data

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    Sample components

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    Entire SOSIP gp140 KNH1144 17b

    EntireName: SOSIP gp140 KNH1144 17b / Number of components: 4 / Oligomeric State: trimeric

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    Component #1: protein, SOSIP gp140 KNH1144 17b

    ProteinName: SOSIP gp140 KNH1144 17b / Recombinant expression: Yes
    SourceSpecies: Human immunodeficiency virus 1 / virus

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: NONE / Cryogen name: ETHANE

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    Electron microscopy imaging

    ImagingMicroscope: FEI POLARA 300
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
    LensImaging mode: BRIGHT FIELD
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN

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    Image processing

    ProcessingMethod: subtomogram averaging
    3D reconstructionResolution: 20 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: Chimera / Refinement space: REAL
    Input PDB model: 3DNO

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