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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
#1: Surface view with section colored by density value, Surface level: 0.045, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 0.045, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1964 |
|---|---|
| Authors | Chen S, Bubeck D, MacDonald BT, Liang WX, Mao JH, Malinauskas T, Llorca O, Aricescu AR, Siebold C, He X, Jones EY |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.045, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.045, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Dev. Cell, Vol. 21, Issue 5, Page 848-61, Year 2011 |
|---|---|
| Title | Structural and functional studies of LRP6 ectodomain reveal a platform for Wnt signaling. |
| Authors | 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 Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. |
| Keywords |  Crystallography, 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 |
| Links | DOI: 10.1016/j.devcel.2011.09.007, PubMed: 22000855, PMC: PMC3564486 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1964.map ( map file in CCP4 format, 866 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 273.6 A , B = 273.6 A , C = 273.6 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 4.56 A , Y = 4.56 A , Z = 4.56 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is a surface rendering of the LRP6 ectodomain filtered to 25 angstroms resolution. | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Ectodomain of LRP6 residues 20 to 1361 |
|---|---|
| Number of Components | 1 |
| Oligomeric State | Monomer |
| Details | The sample was monodisperse |
| Mass-estimation Method | Multi angle light scattering |
| Experimental Mass | 0.165 MDa |
| Component #1: protein - LRP6 | |
| Scientific name | LDL-receptor-related protein 6 |
| Common Name | LRP6 |
| Experimental Mass | 0.165 MDa |
| Oligomeric Details | monomer |
| Number of Copies | 1 |
| Scientific Name of Species | Homo sapiens (NCBI Taxonomy: 9606) |
| Common Name of Species | Human |
| Recombinant expression | Yes |
| Engineered Source | Vector: pHLsec vector Exp System: Homo sapiens embryonic kidney cells |
 Experiment | |
| Sample Preparation | |
| Staining | Grids were negatively stained with 0.75% uranyl formate using the two-drop method |
|---|---|
| Specimen Conc | 0.030 mg/ml |
| Specimen Support Details | carbon-coated copper grids |
| Specimen State | particle |
| Buffer | Details: 150 mM NaCl, 50 mM NaAc pH: 5.0 |
| Vitrification | |
| Cryogen Name | NONE |
| Instrument | NONE |
| Imaging | |
| Microscope | JEOL 1230 |
| Electron Gun | |
| Electron Source | LAB6 |
| Accelerating Voltage | 100 kV |
| Electron Dose | 10 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 72500 X, |
| Nominal Cs | 2.9 mm |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder | |
| Holder | single-tilt ( JEOL ) |
| Camera | |
| Detector | TemCam-F416 camera from TVIPS |
| Image Acquisition | |
| Sampling Size | 4.56 microns |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | angular reconstitution |
| Software | EMAN, XMIPP |
| Resolution By Author | 25 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 6999 |
| Atomic Model Fitting | |
| Model #0 | |
| 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 . |
| Software | Coot |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1964.xml (7.6 KB) | ||
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| Map data | emd_1964.map.gz (791.8 KB) | ||
| Images |  1964_LRP6_2.jpg (33.7 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1964 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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