+Open data
-Basic information
Entry | Database: PDB / ID: 8ffm | ||||||
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Title | Wildtype rat TRPV2 in nanodiscs bound to RR and 2-APB | ||||||
Components | Transient receptor potential cation channel subfamily V member 2 | ||||||
Keywords | MEMBRANE PROTEIN / TRPV2 / 2-APB / TRP Channel / Ruthenium Red | ||||||
Function / homology | Function and homology information growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / positive regulation of axon extension / endomembrane system / axonal growth cone / monoatomic cation channel activity / calcium channel activity / positive regulation of cold-induced thermogenesis ...growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / positive regulation of axon extension / endomembrane system / axonal growth cone / monoatomic cation channel activity / calcium channel activity / positive regulation of cold-induced thermogenesis / melanosome / lamellipodium / 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: 2.9 Å | ||||||
Authors | Pumroy, R.A. / Protopopova, A.D. / Rocereta, J.A. / De Jesus-Perez, J.J. / Fluck, E.C. / Moiseenkova-Bell, V.Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: EMBO Rep / Year: 2024 Title: Molecular details of ruthenium red pore block in TRPV channels. Authors: Ruth A Pumroy / José J De Jesús-Pérez / Anna D Protopopova / Julia A Rocereta / Edwin C Fluck / Tabea Fricke / Bo-Hyun Lee / Tibor Rohacs / Andreas Leffler / Vera Moiseenkova-Bell / Abstract: Transient receptor potential vanilloid (TRPV) channels play a critical role in calcium homeostasis, pain sensation, immunological response, and cancer progression. TRPV channels are blocked by ...Transient receptor potential vanilloid (TRPV) channels play a critical role in calcium homeostasis, pain sensation, immunological response, and cancer progression. TRPV channels are blocked by ruthenium red (RR), a universal pore blocker for a wide array of cation channels. Here we use cryo-electron microscopy to reveal the molecular details of RR block in TRPV2 and TRPV5, members of the two TRPV subfamilies. In TRPV2 activated by 2-aminoethoxydiphenyl borate, RR is tightly coordinated in the open selectivity filter, blocking ion flow and preventing channel inactivation. In TRPV5 activated by phosphatidylinositol 4,5-bisphosphate, RR blocks the selectivity filter and closes the lower gate through an interaction with polar residues in the pore vestibule. Together, our results provide a detailed understanding of TRPV subfamily pore block, the dynamic nature of the selectivity filter and allosteric communication between the selectivity filter and lower gate. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ffm.cif.gz | 540.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ffm.ent.gz | 403.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ffm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ffm_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8ffm_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8ffm_validation.xml.gz | 75.8 KB | Display | |
Data in CIF | 8ffm_validation.cif.gz | 115.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/8ffm ftp://data.pdbj.org/pub/pdb/validation_reports/ff/8ffm | HTTPS FTP |
-Related structure data
Related structure data | 29047MC 8fflC 8ffnC 8ffqC 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 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9WUD2 #2: Chemical | ChemComp-PEX / #3: Chemical | ChemComp-FZ4 / #4: Chemical | ChemComp-R2R / | 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: Tetramer of wildtype rat TRPV2 in nanodiscs bound to ruthenium red Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.34 MDa / Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 8 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | 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 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 defocus max: 20000 nm / Nominal defocus min: 5000 nm |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 10643 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 690077 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65741 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7n0m Accession code: 7n0m / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE |