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    Yorodumi
    - EMDB-1964: Structural and Functional Studies of LRP6 Ectodomain Reveal a Pla... -

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    Basic information

    Entry
    Database: EMDB / ID: 1964
    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
    SourceHomo sapiens / human
    Map dataThis is a surface rendering of the LRP6 ectodomain filtered to 25 angstroms resolution.
    Methodsingle particle reconstruction, at 25 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: 0.045
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 0.045
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1964.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:0.045 (by author), 0.045 (movie #1):
    Minimum - Maximum-0.03536855 - 0.1769339
    Average (Standard dev.)0.00048734 (0.01180683)
    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-0.0350.1770.000

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    Supplemental data

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    Sample components

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    Entire Ectodomain of LRP6 residues 20 to 1361

    EntireName: Ectodomain of LRP6 residues 20 to 1361 / Details: The sample was monodisperse / Number of components: 1 / Oligomeric State: Monomer
    MassExperimental: 165 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 / Recombinant expression: Yes / Number of Copies: 1
    MassExperimental: 165 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Homo sapiens embryonic kidney cells / human
    Vector: pHLsec vector

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.03 mg/ml / Buffer solution: 150 mM NaCl, 50 mM NaAc / pH: 5
    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: 6999 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: angular reconstitution / Software: EMAN, XMIPP / Resolution: 25 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: Coot / Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: Rigid Body. A homology model of LRP6 residues 20 to 1244 based on the LRP6P3E3P4E4 crystal structure was built using Modeller. This single rigid-body was manually docked into the electron microscopy reconstruction and subjected to automated real-space refinement in Coot. Residues linking E2 and P3 residues 628 to 632 were removed. The model was subsequently refined as two rigid bodies residues 20 to 627 and residues 633 to 1244 using Coot. Refined models were scored against the electron microscopy map using a real space correlation coefficient computing using the Bsoft package .
    Input PDB model: 4A0P

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