|Entry||Database: EMDB / ID: 6824|
|Title||structure of endo-lysosomal TRPML1 channel inserting into amphipol: state 2|
|Map data||amphipol state 2|
|Sample||mammalian endo-lysosomal TRPML1 channel inserting into amphipol:|
|Function / homology||Polycystin cation channel / Transferrin endocytosis and recycling / Polycystin cation channel, PKD1/PKD2 / TRP channels / cation transmembrane transport / intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity / ligand-gated calcium channel activity / NAADP-sensitive calcium-release channel activity / cellular response to pH / cation channel activity ...Polycystin cation channel / Transferrin endocytosis and recycling / Polycystin cation channel, PKD1/PKD2 / TRP channels / cation transmembrane transport / intracellular phosphatidylinositol-3,5-bisphosphate-sensitive cation channel activity / ligand-gated calcium channel activity / NAADP-sensitive calcium-release channel activity / cellular response to pH / cation channel activity / phagocytic cup / autophagosome maturation / late endosome membrane / calcium ion transmembrane transport / cell projection / endosomal transport / cellular response to calcium ion / lysosomal membrane / phagocytic vesicle membrane / late endosome / adaptive immune response / receptor complex / protein homotetramerization / lysosome / lipid binding / membrane / integral component of membrane / plasma membrane / cytosol / Mucolipin-1|
Function and homology information
|Source||Mus musculus (house mouse)|
|Method||single particle reconstruction / cryo EM / 5.8 Å resolution|
|Authors||Yang M / Gao N|
|Citation||Journal: Protein Cell / Year: 2017|
Title: Cryo-EM structures of the mammalian endo-lysosomal TRPML1 channel elucidate the combined regulation mechanism.
Authors: Sensen Zhang / Ningning Li / Wenwen Zeng / Ning Gao / Maojun Yang
|Validation Report||PDB-ID: 5ye1|
SummaryFull reportAbout validation report
|Date||Deposition: Sep 15, 2017 / Header (metadata) release: Dec 27, 2017 / Map release: Dec 27, 2017 / Last update: Dec 27, 2017|
|Structure viewer||EM map: |
Downloads & links
|File||emd_6824.map.gz (map file in CCP4 format, 1373 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.64 Å|
CCP4 map header:
-Entire mammalian endo-lysosomal TRPML1 channel inserting into amphipol
|Entire||Name: mammalian endo-lysosomal TRPML1 channel inserting into amphipol|
Number of components: 2
-Component #1: cellular-component, mammalian endo-lysosomal TRPML1 channel inser...
|Cellular-component||Name: mammalian endo-lysosomal TRPML1 channel inserting into amphipol|
Recombinant expression: No
|Source||Species: Mus musculus (house mouse)|
|Source (engineered)||Expression System: Homo sapiens (human)|
-Component #2: protein, Mucolipin-1
|Protein||Name: Mucolipin-1MCOLN1 / Recombinant expression: No|
|Mass||Theoretical: 65.573617 kDa|
|Source (engineered)||Expression System: Mus musculus (house mouse)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Cryogen name: ETHANE|
-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: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 167000|
|3D reconstruction||Software: RELION / Resolution: 5.8 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