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- EMDB-7127: Structure of the cold- and menthol-sensing ion channel TRPM8 -

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Basic information

Entry
Database: EMDB / ID: EMD-7127
TitleStructure of the cold- and menthol-sensing ion channel TRPM8
Map dataSingle-particle cryo-EM reconstruction of Transient Receptor Potential Melastatin channel TRPM8.
Sample
  • Complex: Transient receptor potential cation channel subfamily M member 8 (TRPM8)
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8
Keywordscold sensor / menthol sensor / calcium-permeable ion channel / ion channel / TRANSPORT PROTEIN
Function / homologyTRPM, SLOG domain / : / SLOG in TRPM / monoatomic ion channel activity / Ion transport domain / Ion transport protein / identical protein binding / membrane / Transient receptor potential cation channel subfamily M member 8
Function and homology information
Biological speciesFicedula albicollis (Collared flycatcher)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
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.
History
DepositionNov 25, 2017-
Header (metadata) releaseDec 13, 2017-
Map releaseDec 13, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

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

emd_7127.png

Downloads & links

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Map

FileDownload / File: emd_7127.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle-particle cryo-EM reconstruction of Transient Receptor Potential Melastatin channel TRPM8.
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.14530556 - 0.25385612
Average (Standard dev.)0.0004807912 (±0.010748679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90.0 °

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

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Supplemental data

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Half map: Odd half map

Fileemd_7127_half_map_1.map
AnnotationOdd half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Even half map

Fileemd_7127_half_map_2.map
AnnotationEven half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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

EntireName: Transient receptor potential cation channel subfamily M member 8 (TRPM8)
Components
  • Complex: Transient receptor potential cation channel subfamily M member 8 (TRPM8)
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 8

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Supramolecule #1: Transient receptor potential cation channel subfamily M member 8 ...

SupramoleculeName: Transient receptor potential cation channel subfamily M member 8 (TRPM8)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ficedula albicollis (Collared flycatcher)

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Macromolecule #1: Transient receptor potential cation channel subfamily M member 8

MacromoleculeName: Transient receptor potential cation channel subfamily M member 8
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Ficedula albicollis (Collared flycatcher)
Molecular weightTheoretical: 107.845281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)CDTDSETLY DLMTQHWHLK TPNLVISVTG GAKNFALKPR MRKIFSRLIY IAQSKGAWIF T GGTHYGLM KYIGEVVRDN ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)CDTDSETLY DLMTQHWHLK TPNLVISVTG GAKNFALKPR MRKIFSRLIY IAQSKGAWIF T GGTHYGLM KYIGEVVRDN TISRSSEENV VAIGIA(UNK)(UNK)(UNK)(UNK) (UNK)LKRDPLYCL DNNHTHLLLV DN GTHGHPT IEAKVRTQLE KYISERVIPE SNYGGKIPIV CFAQGGGKET LKSINVAIKS KIPCVVVEGS GRIADVIASL VEA EGTLAS SCVKESLLRF LPRTISRLSE EETESWIKWI KEVLESPHLL TVIKIEEAGD EIVSNAISFA LYKAFSTNEH DRDN WNGQL KLLLEWNQLD LASDEIFTND RNWESADLQD VMFTALVKDR PKFVRLFLEN GLNLRKFLTT EVLRELYTNN FSSLV FKNL QIAKNSYNDA LLTFVWKMVE DFRRGAKRDD KNSKDEMEIE LSEECPITRH PLQALFIWSV LQNKKELSKV IWEQTR GCT LAALGASKLL KSMAKVKNDI NAAGESEELA NEYETRAVEL FTECYSNDED LAEQLLTYSC EAWGGSNCLE LAVEARD QQ FIAQPGVQNF LSKQWYGEIS RDTKNWKIIL CLFFFPLIGC GFISFRKKPV EKTKKLFLYY VSFFTSPFVV FSWNVIFY I AFLLLFAYVL LMDFQKEPTA LEIILYVLVF ILLCDEVRQW YMNGSKYFSD LWNVMDTLAI FYFIAGIVFR LHSDESSWY SGRVIFCLDY IVFTLRLIHI FTVSRNLGPK IIMLQRMMID VFFFLFLFAV WMVAFGVARQ GILRKNEHRW EWIFRSVIYE PYLAMFGQY PDDIDGTTYN FDHCTFSGNE SKPLCVELDA NNQPRFPEWI TIPLVCIYML STNILLVNLL VAMFGYTVGS V QENNDQVW KFQRFFLVQE YCSRLT(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)RNEDN EILAWEAVMK ENYLVKINT(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-48 / Number real images: 8367 / Average exposure time: 12.0 sec. / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3142841
Startup modelType of model: OTHER
Details: A 3D reconstruction of TRPM8 was obtained from pilot cryo-EM studies using a 60-Angstrom low-pass filtered map of EMD-8764. An initial model was generated from this 3D reconstruction low- ...Details: A 3D reconstruction of TRPM8 was obtained from pilot cryo-EM studies using a 60-Angstrom low-pass filtered map of EMD-8764. An initial model was generated from this 3D reconstruction low-pass filtered to 30 Angstrom resolution.
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1b1) / Number images used: 19740
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1b1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1b1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 96
Output model

PDB-6bpq:
Structure of the cold- and menthol-sensing ion channel TRPM8

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