|Entry||Database: EMDB / ID: 7127|
|Title||Structure of the cold- and menthol-sensing ion channel TRPM8|
|Map data||Single-particle cryo-EM reconstruction of Transient Receptor Potential Melastatin channel TRPM8.|
|Sample||Transient receptor potential cation channel subfamily M member 8 (TRPM8)|
|Function / homology||Ion transport domain / Transient receptor potential cation channel subfamily M member 8 / Ion transport protein / detection of temperature stimulus / sensory perception of temperature stimulus / cation transport / ion channel activity / integral component of membrane / plasma membrane / Transient receptor potential cation channel subfamily M member 8|
Function and homology information
|Source||Ficedula albicollis (collared flycatcher)|
|Method||single particle reconstruction / cryo EM / 4.1 Å resolution|
|Authors||Yin Y / Wu M|
|Citation||Journal: Science / Year: 2018|
Title: Structure of the cold- and menthol-sensing ion channel TRPM8.
Authors: Ying Yin / Mengyu Wu / Lejla Zubcevic / William F Borschel / Gabriel C Lander / Seok-Yong Lee
Abstract: Transient receptor potential melastatin (TRPM) cation channels are polymodal sensors that are involved in a variety of physiological processes. Within the TRPM family, member 8 (TRPM8) is the primary ...Transient receptor potential melastatin (TRPM) cation channels are polymodal sensors that are involved in a variety of physiological processes. Within the TRPM family, member 8 (TRPM8) is the primary cold and menthol sensor in humans. We determined the cryo-electron microscopy structure of the full-length TRPM8 from the collared flycatcher at an overall resolution of ~4.1 ångstroms. Our TRPM8 structure reveals a three-layered architecture. The amino-terminal domain with a fold distinct among known TRP structures, together with the carboxyl-terminal region, forms a large two-layered cytosolic ring that extensively interacts with the transmembrane channel layer. The structure suggests that the menthol-binding site is located within the voltage-sensor-like domain and thus provides a structural glimpse of the design principle of the molecular transducer for cold and menthol sensation.
Copyright: 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
|Validation Report||PDB-ID: 6bpq|
SummaryFull reportAbout validation report
|Date||Deposition: Nov 25, 2017 / Header (metadata) release: Dec 13, 2017 / Map release: Dec 13, 2017 / Last update: Mar 7, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_7127.map.gz (map file in CCP4 format, 67109 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.31 Å|
CCP4 map header:
-Entire Transient receptor potential cation channel subfamily M member 8 ...
|Entire||Name: Transient receptor potential cation channel subfamily M member 8 (TRPM8)|
Number of components: 2
-Component #1: protein, Transient receptor potential cation channel subfamily M ...
|Protein||Name: Transient receptor potential cation channel subfamily M member 8 (TRPM8)|
Recombinant expression: No
|Source||Species: Ficedula albicollis (collared flycatcher)|
|Source (engineered)||Expression System: Homo sapiens (human)|
-Component #2: protein, Transient receptor potential cation channel subfamily M ...
|Protein||Name: Transient receptor potential cation channel subfamily M member 8|
Recombinant expression: No
|Mass||Theoretical: 107.845281 kDa|
|Source (engineered)||Expression System: Ficedula albicollis (collared flycatcher)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.5 mg/ml / pH: 8|
|Support film||15 mA|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 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: 56 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 22500 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 2000 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 8367 / Sampling size: 5 microns|
-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.
- 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.: 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