+Open data
-Basic information
Entry | Database: PDB / ID: 8sly | |||||||||
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Title | Rat TRPV2 bound with 2 CBD ligands in nanodiscs | |||||||||
Components | Transient receptor potential cation channel subfamily V member 2 | |||||||||
Keywords | MEMBRANE PROTEIN / Transport protein | |||||||||
Function / homology | Function and homology information growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / endomembrane system / positive regulation of axon extension / monoatomic cation channel activity / axonal growth cone / calcium channel activity / melanosome ...growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / endomembrane system / positive regulation of axon extension / monoatomic cation channel activity / axonal growth cone / calcium channel activity / melanosome / lamellipodium / positive regulation of cold-induced thermogenesis / cell body / negative regulation of cell population proliferation / axon / cell surface / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å | |||||||||
Authors | Tan, X. / Swartz, K.J. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2023 Title: Cannabidiol sensitizes TRPV2 channels to activation by 2-APB. Authors: Aaron Gochman / Xiao-Feng Tan / Chanhyung Bae / Helen Chen / Kenton J Swartz / Andres Jara-Oseguera / Abstract: The cation-permeable TRPV2 channel is important for cardiac and immune cell function. Cannabidiol (CBD), a non-psychoactive cannabinoid of clinical relevance, is one of the few molecules known to ...The cation-permeable TRPV2 channel is important for cardiac and immune cell function. Cannabidiol (CBD), a non-psychoactive cannabinoid of clinical relevance, is one of the few molecules known to activate TRPV2. Using the patch-clamp technique, we discover that CBD can sensitize current responses of the rat TRPV2 channel to the synthetic agonist 2-aminoethoxydiphenyl borate (2-APB) by over two orders of magnitude, without sensitizing channels to activation by moderate (40°C) heat. Using cryo-EM, we uncover a new small-molecule binding site in the pore domain of rTRPV2 in addition to a nearby CBD site that had already been reported. The TRPV1 and TRPV3 channels are also activated by 2-APB and CBD and share multiple conserved features with TRPV2, but we find that strong sensitization by CBD is only observed in TRPV3, while sensitization for TRPV1 is much weaker. Mutations at non-conserved positions between rTRPV2 and rTRPV1 in either the pore domain or the CBD sites failed to confer strong sensitization by CBD in mutant rTRPV1 channels. Together, our results indicate that CBD-dependent sensitization of rTRPV2 channels engages multiple channel regions, and that the difference in sensitization strength between rTRPV2 and rTRPV1 channels does not originate from amino acid sequence differences at the CBD binding site or the pore domain. The remarkably robust effect of CBD on TRPV2 and TRPV3 channels offers a promising new tool to both understand and overcome one of the major roadblocks in the study of these channels - their resilience to activation. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sly.cif.gz | 416.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sly.ent.gz | 331.3 KB | Display | PDB format |
PDBx/mmJSON format | 8sly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sly_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8sly_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8sly_validation.xml.gz | 70.4 KB | Display | |
Data in CIF | 8sly_validation.cif.gz | 101.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/8sly ftp://data.pdbj.org/pub/pdb/validation_reports/sl/8sly | HTTPS FTP |
-Related structure data
Related structure data | 40583MC 8slxC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 86798.891 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpv2, Sac2b, Vrl1 / Cell line (production host): HEK / Production host: Homo sapiens (human) / Strain (production host): TSA201 / References: UniProt: Q9WUD2 #2: Chemical | ChemComp-P0T / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-POV / ( #5: Water | ChemComp-HOH / | 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: Trpv2 with CBD ligand / Type: CELL / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) / Strain: tsa201 |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43071 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.11 Å2 | ||||||||||||||||||||||||
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