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    Yorodumi
    - EMDB-5288: The single particle reconstruction of the human Toll-like recepto... -

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    Basic information

    Entry
    Database: EMDB / ID: 5288
    TitleThe single particle reconstruction of the human Toll-like receptor 5 ectodomain in detergent
    KeywordsToll-like receptor 5 / ectodomain
    Sampletoll-like receptor 5 ectodomain
    SourceHomo sapiens / human
    Map dataThis is the volume of the hTLR5 ectodomain.
    Methodsingle particle reconstruction, at 26 A resolution
    AuthorsZhou K / Kanai R / Lee P / Wang HW / Modis Y
    CitationJ. Struct. Biol., 2012, 177, 402-409

    J. Struct. Biol., 2012, 177, 402-409 StrPapers
    Toll-like receptor 5 forms asymmetric dimers in the absence of flagellin.
    Kaifeng Zhou / Ryuta Kanai / Phong Lee / Hong-Wei Wang / Yorgo Modis

    DateDeposition: May 2, 2011 / Header (metadata) release: May 5, 2011 / Map release: Dec 19, 2011 / Last update: May 2, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 3.57
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 3.57
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_5288.map.gz (map file in CCP4 format, 3908 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    100 pix
    2.14 A/pix
    = 214. A
    100 pix
    2.14 A/pix
    = 214. A
    100 pix
    2.14 A/pix
    = 214. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.14 A
    Density
    Contour Level:3.57 (by author), 3.57 (movie #1):
    Minimum - Maximum-5.61073 - 11.9316
    Average (Standard dev.)9.24672e-10 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions100100100
    Origin000
    Limit999999
    Spacing100100100
    CellA=B=C: 214 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.142.142.14
    M x/y/z100100100
    origin x/y/z0.0000.0000.000
    length x/y/z214.000214.000214.000
    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-5.61111.9320.000

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    Supplemental data

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    Sample components

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    Entire toll-like receptor 5 ectodomain

    EntireName: toll-like receptor 5 ectodomain / Details: The sample was monodisperse / Number of components: 2 / Oligomeric State: dimer
    MassTheoretical: 200 kDa / Experimental: 200 kDa / Measured by: gel filtration

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    Component #1: protein, Toll-like receptor

    ProteinName: Toll-like receptor / a.k.a: TLR5 / Oligomeric Details: dimer / Recombinant expression: Yes / Number of Copies: 2
    MassTheoretical: 200 kDa / Experimental: 200 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Sf9 insect cells / Vector: pAcGP67-A
    Source (natural)Organelle: membrane / Location in cell: plasma membrane / Cell: Sf9 insect cells
    External referencesInterPro: InterPro: 017241

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.005 mg/ml / Buffer solution: 10 mM TEA, 0.15 M NaCl / pH: 7.5
    Support filmthin carbon covered home-made holey carbon on 400 mesh copper grid
    StainingThe protein solution was applied onto a thin-carbon-covered holey carbon copper grid and negatively stained in 1% uranyl-formate solution for 1 minute.
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 12 / Date: Aug 1, 2010
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
    LensMagnification: 52000 X (nominal), 52000 X (calibrated) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 1200 nm
    Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC
    CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 50

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 100 / Number of projections: 3087 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Random conical tilt followed by projection matching refinement
    Software: IMAGIC SPIDER
    Details: Final maps were calculated from all the particles by back-projection reconstruction.
    Resolution: 26 A / Resolution method: FSC 0.5

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