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Yorodumi- PDB-7mik: Mouse TRPV3 in MSP2N2 nanodiscs, closed state at 42 degrees Celsius -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mik | |||||||||||||||
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Title | Mouse TRPV3 in MSP2N2 nanodiscs, closed state at 42 degrees Celsius | |||||||||||||||
Components | Transient receptor potential cation channel subfamily V member 3 | |||||||||||||||
Keywords | MEMBRANE PROTEIN / Transient Receptor Potential V Family Member 3 / TRP channel / TRPV3 / closed state at 42 degrees Celsius / MSP2N2 | |||||||||||||||
Function / homology | Function and homology information negative regulation of hair cycle / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic cation channel activity / monoatomic ion channel activity / calcium channel activity / lysosome / receptor complex / membrane ...negative regulation of hair cycle / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic cation channel activity / monoatomic ion channel activity / calcium channel activity / lysosome / receptor complex / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||||||||
Authors | Nadezhdin, K.D. / Neuberger, A. / Sobolevsky, A.I. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Structural mechanism of heat-induced opening of a temperature-sensitive TRP channel. Authors: Kirill D Nadezhdin / Arthur Neuberger / Yuri A Trofimov / Nikolay A Krylov / Viktor Sinica / Nikita Kupko / Viktorie Vlachova / Eleonora Zakharian / Roman G Efremov / Alexander I Sobolevsky / Abstract: Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been ...Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been studied extensively, structural determination of their heat- and cold-activated states has remained a challenge. Here, we present cryo-EM structures of the nanodisc-reconstituted wild-type mouse TRPV3 in three distinct conformations: closed, heat-activated sensitized and open states. The heat-induced transformations of TRPV3 are accompanied by changes in the secondary structure of the S2-S3 linker and the N and C termini and represent a conformational wave that links these parts of the protein to a lipid occupying the vanilloid binding site. State-dependent differences in the behavior of bound lipids suggest their active role in thermo-TRP temperature-dependent gating. Our structural data, supported by physiological recordings and molecular dynamics simulations, provide an insight for understanding the molecular mechanism of temperature sensing. | |||||||||||||||
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 | 7mik.cif.gz | 488.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mik.ent.gz | 426.5 KB | Display | PDB format |
PDBx/mmJSON format | 7mik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mik_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7mik_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7mik_validation.xml.gz | 92.4 KB | Display | |
Data in CIF | 7mik_validation.cif.gz | 124.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/7mik ftp://data.pdbj.org/pub/pdb/validation_reports/mi/7mik | HTTPS FTP |
-Related structure data
Related structure data | 23854MC 7mijC 7milC 7mimC 7minC 7mioC 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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1 |
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-Components
#1: Protein | Mass: 92630.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trpv3 / Production host: Homo sapiens (human) / References: UniProt: Q8K424 #2: Chemical | ChemComp-POV / ( #3: Chemical | ChemComp-NA / Has ligand of interest | N | |
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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 V member 3 Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.9247 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -2000 nm / Nominal defocus min: -800 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 2.5 sec. / Electron dose: 58.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 20408 |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5855393 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54146 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL |