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Open data
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Basic information
Entry | Database: PDB / ID: 7lqz | |||||||||||||||
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Title | Structure of squirrel TRPV1 in complex with RTX | |||||||||||||||
![]() | Osm-9-like TRP channel 1 | |||||||||||||||
![]() | MEMBRANE PROTEIN / Transient Receptor Potential V Family Member 1 / TRP channel / TRPV1 full length / TRPV1 wild type / RTX / resiniferatoxin | |||||||||||||||
Function / homology | ![]() temperature-gated ion channel activity / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / cellular response to acidic pH / fever generation / detection of temperature stimulus involved in thermoception / dendritic spine membrane ...temperature-gated ion channel activity / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / cellular response to acidic pH / fever generation / detection of temperature stimulus involved in thermoception / dendritic spine membrane / calcium ion import across plasma membrane / diet induced thermogenesis / behavioral response to pain / detection of temperature stimulus involved in sensory perception of pain / extracellular ligand-gated monoatomic ion channel activity / phosphoprotein binding / calcium channel activity / lipid metabolic process / cellular response to heat / postsynaptic membrane / calmodulin binding / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||||||||
![]() | Neuberger, A. / Nadezhdin, K.D. / Sobolevsky, A.I. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Extracellular cap domain is an essential component of the TRPV1 gating mechanism. Authors: Kirill D Nadezhdin / Arthur Neuberger / Yury A Nikolaev / Lyle A Murphy / Elena O Gracheva / Sviatoslav N Bagriantsev / Alexander I Sobolevsky / ![]() Abstract: Transient receptor potential (TRP) channels are polymodal molecular sensors involved in numerous physiological processes and implicated in a variety of human diseases. Several structures of the ...Transient receptor potential (TRP) channels are polymodal molecular sensors involved in numerous physiological processes and implicated in a variety of human diseases. Several structures of the founding member of the TRP channel family, TRPV1, are available, all of which were determined for the protein missing the N- and C-termini and the extracellular S5-P-loop. Here, we present structures of the full-length thirteen-lined ground squirrel TRPV1 solved by cryo-EM. Our structures resolve the extracellular cap domain formed by the S5-P-loops and the C-terminus that wraps around the three-stranded β-sheet connecting elements of the TRPV1 intracellular skirt. The cap domain forms a dome above the pore's extracellular entrance, with four portals leading to the ion conductance pathway. Deletion of the cap increases the TRPV1 average conductance, reduces the open probability and affects ion selectivity. Our data show that both the termini and the cap domain are critical determinants of TRPV1 function. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 506.2 KB | Display | ![]() |
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PDB format | ![]() | 419.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 23492MC ![]() 7lqyC ![]() 7lr0C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 95902.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: TRPV1 / Plasmid: pEG BacMam / Cell line (production host): HEK293 / Production host: ![]() #2: Chemical | ChemComp-POV / ( #3: Chemical | ChemComp-6EU / #4: Chemical | ChemComp-NA / | 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 |
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Sample preparation
Component | Name: sample 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3 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 |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -3500 nm / Nominal defocus min: -1500 nm / Cs: 2 mm |
Image recording | Average exposure time: 2.5 sec. / Electron dose: 70.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3253 |
EM imaging optics | Energyfilter slit width: 30 eV |
Image scans | Width: 5760 / Height: 4092 |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1391804 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 333521 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL |