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

by single particle reconstruction, at 25 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.045, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.045, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1964
TitleStructural and Functional Studies of LRP6 Ectodomain Reveal a Platform for Wnt Signaling
MapThis is a surface rendering of the LRP6 ectodomain filtered to 25 angstroms resolution.
SampleEctodomain of LRP6 residues 20 to 1361
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: 0.045, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.045, 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_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.

Density
Contour Level:0.045 (by author), 0.045 (movie #1):
Minimum - Maximum: -0.03536855 - 0.1769339
Average (Standard dev.): 0.00048734 (0.01180683)
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-0.0350.1770.000
Annotation DetailsThis is a surface rendering of the LRP6 ectodomain filtered to 25 angstroms resolution.
Supplement
Images
Images
Sample
NameEctodomain of LRP6 residues 20 to 1361
Number of Components1
Oligomeric StateMonomer
DetailsThe sample was monodisperse
Mass-estimation MethodMulti angle light scattering
Experimental Mass0.165MDa
Component #1: protein - LRP6
Scientific nameLDL-receptor-related protein 6
Common NameLRP6
Experimental Mass0.165 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: Homo sapiens embryonic kidney cells
Experiment
Sample Preparation
StainingGrids were negatively stained with 0.75% uranyl formate using the two-drop method
Specimen Conc0.03 mg/ml
Specimen Support Detailscarbon-coated copper grids
Specimen Stateparticle
BufferDetails: 150 mM NaCl, 50 mM NaAc
pH: 5
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
#1
Sampling Size4.56
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmangular reconstitution
SoftwareEMAN, XMIPP
Resolution By Author25 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections6999
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
DetailsProtocol: 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 .
SoftwareCoot
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID4A0P
Download
Data from EMDB
Header (meta data in XML format)emd-1964.xml (7.7 KB)
Map dataemd_1964.map.gz (791.8 KB)
Images1964_LRP6_2.jpg (33.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1964
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 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), 4.9 MB
Session file for UCSF-Chimera, 26.7 KB