|Entry||Database: EMDB / ID: 7122|
|Title||Cryo-EM structure of human TRPV6-R470E in amphipols|
|Map data||primary map|
|Sample||TRPV6-R470E ion channel in closed states|
|Function / homology||Ion transport domain / Ankyrin repeat / Transient receptor potential channel, vanilloid 6 / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeat-containing domain superfamily / Transient receptor potential channel / Ankyrin repeat / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Ion transport protein ...Ion transport domain / Ankyrin repeat / Transient receptor potential channel, vanilloid 6 / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeat-containing domain superfamily / Transient receptor potential channel / Ankyrin repeat / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Ion transport protein / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / TRP channels / calcium ion import across plasma membrane / regulation of calcium ion-dependent exocytosis / calcium ion homeostasis / calcium channel activity / calcium ion transmembrane transport / calcium ion transport / response to calcium ion / calmodulin binding / integral component of plasma membrane / plasma membrane / metal ion binding / Transient receptor potential cation channel subfamily V member 6|
Function and homology information
|Source||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / 4.2 Å resolution|
|Authors||McGoldrick LL / Singh AK|
|Citation||Journal: Nature / Year: 2018|
Title: Opening of the human epithelial calcium channel TRPV6.
Authors: Luke L McGoldrick / Appu K Singh / Kei Saotome / Maria V Yelshanskaya / Edward C Twomey / Robert A Grassucci / Alexander I Sobolevsky
|Validation Report||PDB-ID: 6boa|
SummaryFull reportAbout validation report
|Date||Deposition: Nov 18, 2017 / Header (metadata) release: Dec 6, 2017 / Map release: Dec 20, 2017 / Last update: Jan 24, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_7122.map.gz (map file in CCP4 format, 35996 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.1 Å|
CCP4 map header:
-Entire TRPV6-R470E ion channel in closed states
|Entire||Name: TRPV6-R470E ion channel in closed states / Number of components: 2|
-Component #1: protein, TRPV6-R470E ion channel in closed states
|Protein||Name: TRPV6-R470E ion channel in closed states / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: HEK-293 cells|
-Component #2: protein, Transient receptor potential cation channel subfamily V ...
|Protein||Name: Transient receptor potential cation channel subfamily V member 6|
Recombinant expression: No
|Mass||Theoretical: 85.140875 kDa|
|Source (engineered)||Expression System: Homo sapiens (human)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.3 mg/ml / Buffer solution: TRIS, NaCl, / pH: 8|
|Vitrification||Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 67 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 59298|
|3D reconstruction||Software: RELION / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
-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
+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
+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.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi