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- 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
  • Download
  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1964.map.gz (map file in CCP4 format, 845 KB)
Projections & slices

Image control

Size
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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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