+Open data
-Basic information
Entry | Database: PDB / ID: 6lgp | ||||||
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Title | cryo-EM structure of TRPV3 in lipid nanodisc | ||||||
Components | Transient receptor potential cation channel subfamily V member 3 | ||||||
Keywords | MEMBRANE PROTEIN / TRP channel / TRPV family / TRPV3 / nanodisc | ||||||
Function / homology | Function and homology information negative regulation of hair cycle / TRP channels / osmosensory signaling pathway / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / monoatomic cation channel activity / actin filament organization / calcium channel activity / cilium ...negative regulation of hair cycle / TRP channels / osmosensory signaling pathway / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / monoatomic cation channel activity / actin filament organization / calcium channel activity / cilium / monoatomic ion channel activity / receptor complex / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Shimada, H. / Kusakizako, T. / Nishizawa, T. / Nureki, O. | ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: The structure of lipid nanodisc-reconstituted TRPV3 reveals the gating mechanism. Authors: Hiroto Shimada / Tsukasa Kusakizako / T H Dung Nguyen / Tomohiro Nishizawa / Tomoya Hino / Makoto Tominaga / Osamu Nureki / Abstract: Transient receptor potential vanilloid subfamily member 3 (TRPV3) is a temperature-sensitive cation channel. Previous cryo-EM analyses of TRPV3 in detergent micelles or amphipol proposed that the ...Transient receptor potential vanilloid subfamily member 3 (TRPV3) is a temperature-sensitive cation channel. Previous cryo-EM analyses of TRPV3 in detergent micelles or amphipol proposed that the lower gate opens by α-to-π helical transitions of the nearby S6 helix. However, it remains unclear how physiological lipids are involved in the TRPV3 activation. Here we determined the apo state structure of mouse (Mus musculus) TRPV3 in a lipid nanodisc at 3.3 Å resolution. The structure revealed that lipids bound to the pore domain stabilize the selectivity filter in the narrow state, suggesting that the selectivity filter of TRPV3 affects cation permeation. When the lower gate is closed in nanodisc-reconstituted TRPV3, the S6 helix adopts the π-helical conformation without agonist- or heat-sensitization, potentially stabilized by putative intra-subunit hydrogen bonds and lipid binding. Our findings provide insights into the lipid-associated gating mechanism of TRPV3. | ||||||
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 | 6lgp.cif.gz | 462.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lgp.ent.gz | 382.4 KB | Display | PDB format |
PDBx/mmJSON format | 6lgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lgp_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6lgp_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6lgp_validation.xml.gz | 77.6 KB | Display | |
Data in CIF | 6lgp_validation.cif.gz | 112.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/6lgp ftp://data.pdbj.org/pub/pdb/validation_reports/lg/6lgp | HTTPS FTP |
-Related structure data
Related structure data | 0882MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10400 (Title: Cryo-EM structure of mouse TRPV3 in a nanodisc / Data size: 2.1 TB Data #1: Unaligned movies for mouse TRPV3 in a nanodisc [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 73949.867 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trpv3 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q8K424 #2: Chemical | ChemComp-POV / ( #3: Chemical | ChemComp-PLC / Has ligand of interest | Y | |
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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: TRPV3 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / 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: 279 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 | ||||||||||||||||
Image recording |
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-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106947 / Symmetry type: POINT | ||||||||||||||||||||||||
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