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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7127 | |||||||||
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Title | Structure of the cold- and menthol-sensing ion channel TRPM8 | |||||||||
![]() | Single-particle cryo-EM reconstruction of Transient Receptor Potential Melastatin channel TRPM8. | |||||||||
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![]() | cold sensor / menthol sensor / calcium-permeable ion channel / ion channel / TRANSPORT PROTEIN | |||||||||
Function / homology | ligand-gated calcium channel activity / : / TRPM, SLOG domain / SLOG in TRPM / Ion transport domain / Ion transport protein / identical protein binding / membrane / Transient receptor potential cation channel subfamily M member 8![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | Yin Y / Wu M | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.8 KB 17.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 196.9 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() | 45.8 MB 45.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bpqMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Single-particle cryo-EM reconstruction of Transient Receptor Potential Melastatin channel TRPM8. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Odd half map
File | emd_7127_half_map_1.map | ||||||||||||
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Annotation | Odd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Even half map
File | emd_7127_half_map_2.map | ||||||||||||
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Annotation | Even half map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Transient receptor potential cation channel subfamily M member 8 ...
Entire | Name: Transient receptor potential cation channel subfamily M member 8 (TRPM8) |
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Components |
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-Supramolecule #1: Transient receptor potential cation channel subfamily M member 8 ...
Supramolecule | Name: Transient receptor potential cation channel subfamily M member 8 (TRPM8) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Transient receptor potential cation channel subfamily M member 8
Macromolecule | Name: Transient receptor potential cation channel subfamily M member 8 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 107.845281 KDa |
Recombinant expression | Organism: ![]() |
Sequence | 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 ...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) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: 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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 96 |
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Output model | ![]() PDB-6bpq: |