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

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Basic information

Entry
Database: PDB / ID: 6bpq
TitleStructure of the cold- and menthol-sensing ion channel TRPM8
ComponentsTransient receptor potential cation channel subfamily M member 8
KeywordsTRANSPORT PROTEIN / cold sensor / menthol sensor / calcium-permeable ion channel / ion channel
Function / homology
Function and homology information


detection of temperature stimulus / sensory perception of temperature stimulus / monoatomic cation transmembrane transport / monoatomic ion channel activity / membrane / identical protein binding
Similarity search - Function
Transient receptor potential cation channel subfamily M member 8 / TRPM, SLOG domain / SLOG in TRPM / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Biological speciesFicedula albicollis (Collared flycatcher)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsYin, Y. / Wu, M. / Zubcevic, L. / Borschel, W.F. / Lander, G.C. / Lee, S.-Y.
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, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily M member 8
B: Transient receptor potential cation channel subfamily M member 8
C: Transient receptor potential cation channel subfamily M member 8
D: Transient receptor potential cation channel subfamily M member 8


Theoretical massNumber of molelcules
Total (without water)431,3814
Polymers431,3814
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 107845.281 Da / Num. of mol.: 4 / Mutation: F535A,Y538D,Y539D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ficedula albicollis (Collared flycatcher)
Gene: TRPM8 / Production host: Homo sapiens (human) / References: UniProt: U3JD03*PLUS
Sequence detailsAuthors state that the sample sequence presented in the structure is of 1135 a.a. residue length, ...Authors state that the sample sequence presented in the structure is of 1135 a.a. residue length, containing N-terminal tag 'MA', full length sequence of UNP entry U3JD03 with F535A, Y538D, Y539D mutations, and C-terminal tag 'SNSLEVLFQGPDYKDDDDKAHHHHHHHHHH'. Poly-UNK residues are modeled at fragments without clear density.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transient receptor potential cation channel subfamily M member 8 (TRPM8)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Ficedula albicollis (Collared flycatcher)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 56 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8367
Image scansSampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 48 / Used frames/image: 1-48

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Processing

EM software
IDNameVersionCategoryDetails
1FindEMparticle selectionTemplate-based correlation
2Leginon3.2image acquisitionAutomated data acquisition software
4CTFFIND4CTF correction
5RELION2.1b1CTF correction
8Coot0.8.8model fitting
10RELION2.1b1initial Euler assignment
11RELION2.1b1final Euler assignment
13RELION2.1b13D reconstruction
20PHENIX1.12-2829-000model refinement
21Coot0.8.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3142841
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19740 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 96 / Protocol: RIGID BODY FIT / Space: REAL

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