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    Yorodumi
    - EMDB-1965: Structural and Functional Studies of LRP6 Ectodomain Reveal a Pla... -

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    Basic information

    Entry
    Database: EMDB / ID: 1965
    TitleStructural and Functional Studies of LRP6 Ectodomain Reveal a Platform for Wnt Signaling
    KeywordsLDL-receptor-related protein 6 / Wnt signaling pathway / Wnt co-receptor
    SampleEctodomain of LRP6 residues 20 to 1361 and chaperone Mesd
    SourceHomo sapiens / human
    Map dataThis is a surface rendering of the ectodomain of LRP6 bound to its chaperone Mesd
    Methodsingle particle reconstruction, at 26 A resolution
    AuthorsChen S / Bubeck D / MacDonald BT / Liang WX / Mao JH / Malinauskas T / Llorca O / Aricescu AR / Siebold C / He X / Jones EY
    CitationDev. Cell, 2011, 21, 848-861

    Dev. Cell, 2011, 21, 848-861 StrPapers
    Structural and functional studies of LRP6 ectodomain reveal a platform for Wnt signaling.
    Shuo Chen / Doryen Bubeck / Bryan T MacDonald / Wen-Xue Liang / Jian-Hua Mao / Tomas Malinauskas / Oscar Llorca / A Radu Aricescu / Christian Siebold / Xi He / E Yvonne Jones

    DateDeposition: Sep 12, 2011 / Header (metadata) release: Sep 30, 2011 / Map release: Oct 21, 2011 / Last update: Sep 12, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.0451
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 0.0451
    • Imaged by UCSF CHIMERA
    • Download
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1965.map.gz (map file in CCP4 format, 845 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    60 pix
    4.56 A/pix
    = 273.6 A
    60 pix
    4.56 A/pix
    = 273.6 A
    60 pix
    4.56 A/pix
    = 273.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.56 A
    Density
    Contour Level:0.0451 (by author), 0.0451 (movie #1):
    Minimum - Maximum-0.0474625 - 0.23142
    Average (Standard dev.)0.00110932 (0.0145592)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions606060
    Origin000
    Limit595959
    Spacing606060
    CellA=B=C: 273.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z4.564.564.56
    M x/y/z606060
    origin x/y/z0.0000.0000.000
    length x/y/z273.600273.600273.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS606060
    D min/max/mean-0.0470.2310.001

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    Supplemental data

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    Sample components

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    Entire Ectodomain of LRP6 residues 20 to 1361 and chaperone Mesd

    EntireName: Ectodomain of LRP6 residues 20 to 1361 and chaperone Mesd
    Details: The sample was monodisperse / Number of components: 2 / Oligomeric State: one LRP6 binds to one Mesd
    MassExperimental: 200 kDa / Measured by: Multi angle light scattering

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    Component #1: protein, LDL-receptor-related protein 6

    ProteinName: LDL-receptor-related protein 6 / a.k.a: LRP6 / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
    MassExperimental: 100 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Hek293s / Vector: pHLsec vector

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    Component #2: protein, Mesoderm development protein

    ProteinName: Mesoderm development protein / a.k.a: Mesd / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
    MassExperimental: 100 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Hek293s / Vector: pHLsec vector

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.015 mg/ml / Buffer solution: 150 mM NaCl,10 mM Tris-HCl / pH: 8
    Support filmcarbon-coated copper grids
    StainingGrids were negatively stained with 0.75% uranyl formate using the two-drop method
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 1230
    Electron gunElectron source: LAB6 / Accelerating voltage: 100 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 72500 X (nominal) / Cs: 2.9 mm / Imaging mode: BRIGHT FIELD
    Specimen HolderHolder: single-tilt / Model: JEOL
    CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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    Image acquisition

    Image acquisitionSampling size: 4.56 microns

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 7928 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: angular reconstitution / Software: EMAN, XMIPP / Resolution: 26 A / Resolution method: FSC 0.5

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