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Structural and Functional Studies of LRP6 Ectodomain Reveal a Platform for Wnt Signaling

by single particle reconstruction, at 26 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0451, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.0451, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1965
TitleStructural and Functional Studies of LRP6 Ectodomain Reveal a Platform for Wnt Signaling
MapThis is a surface rendering of the ectodomain of LRP6 bound to its chaperone Mesd
SampleEctodomain of LRP6 residues 20 to 1361 and chaperone Mesd
KeywordsLDL-receptor-related protein 6, Wnt signaling pathway, Wnt co-receptor
AuthorsChen S, Bubeck D, MacDonald BT, Liang WX, Mao JH, Malinauskas T, Llorca O, Aricescu AR, Siebold C, He X, Jones EY
DateDeposition: 2011-09-12, Header release: 2011-09-30, Map release: 2011-10-21, Last update: 2011-10-21
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0451, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.0451, Made by UCSF CHIMERA

Supplemental images

1965_LRP6_ME...
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
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EMDB-1964
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PDB-4a0p
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Diagram

EMDB-2311

PDB-1if0

PDB-2wwa

EMDB-1213
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleDev. Cell, Vol. 21, Issue 5, Page 848-61, Year 2011
TitleStructural and functional studies of LRP6 ectodomain reveal a platform for Wnt signaling.
AuthorsShuo 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
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
KeywordsCrystallography, X-Ray, HEK293 Cells, Humans, LRP6 protein, human, Low Density Lipoprotein Receptor-Related Protein-6 (chemistry), Models, Molecular, Protein Structure, Tertiary, Wnt Proteins (metabolism), Wnt Signaling Pathway
LinksDOI: 10.1016/j.devcel.2011.09.007, PubMed: 22000855, PMC: PMC3564486
Map
FileEMD-1965.map ( map file in CCP4 format, 866 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.0451 (by author), 0.0451 (movie #1):
Minimum - Maximum: -0.0474625 - 0.23142
Average (Standard dev.): 0.00110932 (0.0145592)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 60 60 60
Origin : 0 0 0
Limit : 59 59 59
Spacing : 60 60 60
Unit CellA = 273.6 A , B = 273.6 A , C = 273.6 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 4.56 A , Y = 4.56 A , Z = 4.56 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0470.2310.001
Annotation DetailsThis is a surface rendering of the ectodomain of LRP6 bound to its chaperone Mesd
Supplement
Images
Images

1965_LRP6_ME...
Sample
NameEctodomain of LRP6 residues 20 to 1361 and chaperone Mesd
Number of Components2
Oligomeric Stateone LRP6 binds to one Mesd
DetailsThe sample was monodisperse
Mass-estimation MethodMulti angle light scattering
Experimental Mass0.2 MDa
Component #1: protein - LRP6
Scientific nameLDL-receptor-related protein 6
Common NameLRP6
Experimental Mass0.1 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens (NCBI Taxonomy: 9606)
Common Name of SpeciesHuman
Recombinant expressionYes
Engineered SourceExp System: HEK293S
Vector: pHLsec vector
Component #2: protein - Mesd
Scientific nameMesoderm development protein
Common NameMesd
Experimental Mass0.1 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesHomo sapiens (NCBI Taxonomy: 9606)
Common Name of SpeciesHuman
Recombinant expressionYes
Engineered SourceVector: pHLsec vector
Exp System: HEK293S
Experiment
Sample Preparation
StainingGrids were negatively stained with 0.75% uranyl formate using the two-drop method
Specimen Conc0.015 mg/ml
Specimen Support Detailscarbon-coated copper grids
Specimen Stateparticle
BufferDetails: 150 mM NaCl,10 mM Tris-HCl
pH: 8.0
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeJEOL 1230
Electron Gun
Electron SourceLAB6
Accelerating Voltage100 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 72500 X,
Nominal Cs2.9 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
Holdersingle-tilt ( JEOL )
Camera
DetectorTemCam-F416 camera from TVIPS
Image Acquisition
Sampling Size4.56 microns
Processing
Methodsingle particle reconstruction
3 D reconstruction
Algorithmangular reconstitution
SoftwareEMAN, XMIPP
Resolution By Author26
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections7928
Download
Data from EMDB
Header (meta data in XML format)emd-1965.xml (7.6 KB)
Map dataemd_1965.map.gz (790.7 KB)
Images1965_LRP6_MESD3.jpg (42.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1965
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.7 KB