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Yorodumi- PDB-6nr4: Cryo-EM structure of the TRPM8 ion channel with low occupancy ici... -
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-Basic information
Entry | Database: PDB / ID: 6nr4 | ||||||
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Title | Cryo-EM structure of the TRPM8 ion channel with low occupancy icilin, PI(4,5)P2, and calcium | ||||||
Components | Transient receptor potential cation channel subfamily M member 8 | ||||||
Keywords | TRANSPORT PROTEIN / ion channel / TRP channel / TRPM channel / TRPM8 channel / cold sensing / lipid sensing / menthol / icilin / WS-12 / PI(4 / 5)P2 / calcium-permeable channel / cooling agent | ||||||
Biological species | Ficedula albicollis (Collared flycatcher) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Yin, Y. / Le, S.C. / Hsu, A.L. / Borgnia, M.J. / Yang, H. / Lee, S.-Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2019 Title: Structural basis of cooling agent and lipid sensing by the cold-activated TRPM8 channel. Authors: Ying Yin / Son C Le / Allen L Hsu / Mario J Borgnia / Huanghe Yang / Seok-Yong Lee / Abstract: Transient receptor potential melastatin member 8 (TRPM8) is a calcium ion (Ca)-permeable cation channel that serves as the primary cold and menthol sensor in humans. Activation of TRPM8 by cooling ...Transient receptor potential melastatin member 8 (TRPM8) is a calcium ion (Ca)-permeable cation channel that serves as the primary cold and menthol sensor in humans. Activation of TRPM8 by cooling compounds relies on allosteric actions of agonist and membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP), but lack of structural information has thus far precluded a mechanistic understanding of ligand and lipid sensing by TRPM8. Using cryo-electron microscopy, we determined the structures of TRPM8 in complex with the synthetic cooling compound icilin, PIP, and Ca, as well as in complex with the menthol analog WS-12 and PIP Our structures reveal the binding sites for cooling agonists and PIP in TRPM8. Notably, PIP binds to TRPM8 in two different modes, which illustrate the mechanism of allosteric coupling between PIP and agonists. This study provides a platform for understanding the molecular mechanism of TRPM8 activation by cooling agents. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6nr4.cif.gz | 554.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nr4.ent.gz | 435.3 KB | Display | PDB format |
PDBx/mmJSON format | 6nr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nr4_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6nr4_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6nr4_validation.xml.gz | 80.9 KB | Display | |
Data in CIF | 6nr4_validation.cif.gz | 125.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/6nr4 ftp://data.pdbj.org/pub/pdb/validation_reports/nr/6nr4 | HTTPS FTP |
-Related structure data
Related structure data | 0489MC 0487C 0488C 6nr2C 6nr3C 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: 129692.938 Da / Num. of mol.: 4 / Mutation: F535A,Y538D,Y539D,A805G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ficedula albicollis (Collared flycatcher) Gene: TRPM8 / Production host: Homo sapiens (human) Sequence details | The complete sample sequence including tags and engineered mutations is the following: ...The complete sample sequence including tags and engineered mutations is the following: MATLFQVSMG | |
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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 melastatin member 8 / 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: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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: 75000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 60 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3705 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1115545 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8700 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 112 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6BPQ | ||||||||||||||||||||||||||||||||||||||||||||||||||
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