[English] 日本語
Yorodumi
- EMDB-7127: Structure of the cold- and menthol-sensing ion channel TRPM8 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 7127
TitleStructure of the cold- and menthol-sensing ion channel TRPM8
Map dataSingle-particle cryo-EM reconstruction of Transient Receptor Potential Melastatin channel TRPM8.
SampleTransient receptor potential cation channel subfamily M member 8 (TRPM8)
  • Transient receptor potential cation channel subfamily M member 8
Function / homologyIon 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
SourceFicedula albicollis (collared flycatcher)
Methodsingle particle reconstruction / cryo EM / 4.1 Å resolution
AuthorsYin Y / Wu M
CitationJournal: 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 ReportPDB-ID: 6bpq

SummaryFull reportAbout validation report
DateDeposition: Nov 25, 2017 / Header (metadata) release: Dec 13, 2017 / Map release: Dec 13, 2017 / Last update: Mar 7, 2018

-
Structure visualization

Movie
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bpq
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_7127.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.31 Å/pix.
= 335.36 Å
256 pix
1.31 Å/pix.
= 335.36 Å
256 pix
1.31 Å/pix.
= 335.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density
Contour Level:0.07 (by author), 0.07 (movie #1):
Minimum - Maximum-0.14530556 - 0.25385612
Average (Standard dev.)0.0004807912 (0.010748679)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z335.360335.360335.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1450.2540.000

-
Supplemental data

-
Sample components

-
Entire Transient receptor potential cation channel subfamily M member 8 ...

EntireName: Transient receptor potential cation channel subfamily M member 8 (TRPM8)
Number of components: 2

-
Component #1: protein, Transient receptor potential cation channel subfamily M ...

ProteinName: Transient receptor potential cation channel subfamily M member 8 (TRPM8)
Recombinant expression: No
SourceSpecies: Ficedula albicollis (collared flycatcher)
Source (engineered)Expression System: Homo sapiens (human)

-
Component #2: protein, Transient receptor potential cation channel subfamily M ...

ProteinName: Transient receptor potential cation channel subfamily M member 8
Recombinant expression: No
MassTheoretical: 107.845281 kDa
Source (engineered)Expression System: Ficedula albicollis (collared flycatcher)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/ml / pH: 8
Support film15 mA
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 56 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 2000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 8367 / Sampling size: 5 microns

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 19740
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more

-
Yorodumi

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

Read more