|Entry||Database: EMDB / ID: 1965|
|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 and chaperone Mesd|
|Source||Homo sapiens / human|
|Map data||This is a surface rendering of the ectodomain of LRP6 bound to its chaperone Mesd|
|Method||single particle reconstruction, at 26 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 StrPapers
|Date||Deposition: Sep 12, 2011 / Header (metadata) release: Sep 30, 2011 / Map release: Oct 21, 2011 / Last update: Sep 12, 2011|
Downloads & links
|File||emd_1965.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 and chaperone Mesd
|Entire||Name: Ectodomain of LRP6 residues 20 to 1361 and chaperone Mesd|
Details: The sample was monodisperse / Number of components: 2 / Oligomeric State: one LRP6 binds to one Mesd
|Mass||Experimental: 200 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 / Number of Copies: 1 / Recombinant expression: Yes|
|Mass||Experimental: 100 kDa|
|Source||Species: Homo sapiens / human|
|Source (engineered)||Expression System: Hek293s / Vector: pHLsec vector|
-Component #2: protein, Mesoderm development protein
|Sample solution||Specimen conc.: 0.015 mg/ml / Buffer solution: 150 mM NaCl,10 mM Tris-HCl / pH: 8|
|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: 7928 / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: angular reconstitution / Software: EMAN, XMIPP / Resolution: 26 Å / Resolution method: FSC 0.5|
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi