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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, Image by UCSF CHIMERA

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

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

Supplemental images
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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.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.

Density
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 orderXYZ
Dimensions606060
Origin000
Limit595959
Spacing606060
Unit CellA= B= C: 273.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= 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
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 Mass0.2MDa
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
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Engineered SourceExpression 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
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Engineered SourceVector: pHLsec vector
Expression 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
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
Nominal Cs2.9 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
Holdersingle-tilt
ModelJEOL
Camera
DetectorTVIPS TEMCAM-F416 (4k x 4k)
Image Acquisition
Sampling Size4.56
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmangular reconstitution
SoftwareEMAN, XMIPP
Resolution By Author26 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections7928
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1965.xml (7.7 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