|Entry||Database: EMDB / ID: 1964|
|Title||Structural and Functional Studies of LRP6 Ectodomain Reveal a Platform for Wnt Signaling|
|Keywords||LDL-receptor-related protein 6 / Wnt signaling pathway / Wnt co-receptor|
|Sample||Ectodomain of LRP6 residues 20 to 1361|
|Source||Homo sapiens / human|
|Map data||This is a surface rendering of the LRP6 ectodomain filtered to 25 angstroms resolution.|
|Method||single particle reconstruction, at 25 Å resolution|
|Authors||Chen S / Bubeck D / MacDonald BT / Liang WX / Mao JH / Malinauskas T / Llorca O / Aricescu AR / Siebold C / He X / Jones EY|
|Citation||Dev. Cell, 2011, 21, 848-861|
Dev. Cell, 2011, 21, 848-861 Yorodumi Papers
|Date||Deposition: Sep 12, 2011 / Header (metadata) release: Sep 30, 2011 / Map release: Oct 21, 2011 / Last update: Oct 21, 2011|
Downloads & links
|File||emd_1964.map.gz (map file in CCP4 format, 845 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 4.56 Å|
CCP4 map header:
-Entire Ectodomain of LRP6 residues 20 to 1361
|Entire||Name: Ectodomain of LRP6 residues 20 to 1361 / Details: The sample was monodisperse / Number of components: 1 / Oligomeric State: Monomer|
|Mass||Experimental: 165 kDa / Measured by: Multi angle light scattering|
-Component #1: protein, LDL-receptor-related protein 6
|Protein||Name: LDL-receptor-related protein 6 / a.k.a: LRP6 / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 1|
|Mass||Experimental: 165 kDa|
|Source||Species: Homo sapiens / human|
|Source (engineered)||Expression System: Homo sapiens embryonic kidney cells / human|
Vector: pHLsec vector
|Sample solution||Specimen conc.: 0.03 mg/ml / Buffer solution: 150 mM NaCl, 50 mM NaAc / pH: 5|
|Support film||carbon-coated copper grids|
|Staining||Grids were negatively stained with 0.75% uranyl formate using the two-drop method|
|Vitrification||Instrument: NONE / Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 1230|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 100 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 72500 X (nominal) / Cs: 2.9 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Holder: single-tilt / Model: JEOL|
|Camera||Detector: TVIPS TEMCAM-F416 (4k x 4k)|
|Image acquisition||Sampling size: 4.56 microns|
|Processing||Method: single particle reconstruction / Number of projections: 6999 / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: angular reconstitution / Software: EMAN, XMIPP / Resolution: 25 Å / Resolution method: FSC 0.5|
-Atomic model buiding
|Modeling #1||Software: Coot / Refinement protocol: rigid body / Refinement space: REAL|
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 .
Input PDB model: 4A0P
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