[English] 日本語
Yorodumi
- EMDB-1965: Structural and Functional Studies of LRP6 Ectodomain Reveal a Pla... -

+
Open data


ID or keywords:

Loading...

no data

-
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

-
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
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
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

-
Supplemental data

-
Sample components

-
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

-
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

-
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

+
Experimental details

-
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

-
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)

-
Image acquisition

Image acquisitionSampling size: 4.56 microns

-
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

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more