+Open data
-Basic information
Entry | Database: PDB / ID: 6bpq | ||||||
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Title | Structure of the cold- and menthol-sensing ion channel TRPM8 | ||||||
Components | Transient receptor potential cation channel subfamily M member 8 | ||||||
Keywords | TRANSPORT PROTEIN / cold sensor / menthol sensor / calcium-permeable ion channel / ion channel | ||||||
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 Function and homology information | ||||||
Biological species | Ficedula albicollis (Collared flycatcher) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Yin, Y. / Wu, M. / Zubcevic, L. / Borschel, W.F. / Lander, G.C. / Lee, S.-Y. | ||||||
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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6bpq.cif.gz | 541.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bpq.ent.gz | 411.7 KB | Display | PDB format |
PDBx/mmJSON format | 6bpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bpq_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6bpq_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6bpq_validation.xml.gz | 84.9 KB | Display | |
Data in CIF | 6bpq_validation.cif.gz | 134.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/6bpq ftp://data.pdbj.org/pub/pdb/validation_reports/bp/6bpq | HTTPS FTP |
-Related structure data
Related structure data | 7127MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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 details | Authors 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 'SNSLEVLFQG | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Transient receptor potential cation channel subfamily M member 8 (TRPM8) Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Ficedula albicollis (Collared flycatcher) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average 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 scans | Sampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 48 / Used frames/image: 1-48 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3142841 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19740 / Algorithm: BACK PROJECTION / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 96 / Protocol: RIGID BODY FIT / Space: REAL |