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Yorodumi- PDB-6bo4: Open state structure of the full-length TRPV2 cation channel with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bo4 | ||||||
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Title | Open state structure of the full-length TRPV2 cation channel with a resolved pore turret domain | ||||||
Components | Transient receptor potential cation channel subfamily V member 2 | ||||||
Keywords | MEMBRANE PROTEIN / channel / TRP / cation / open | ||||||
Function / homology | Function and homology information growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic cation transmembrane transport / endomembrane system / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / calcium channel activity ...growth cone membrane / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic cation transmembrane transport / endomembrane system / positive regulation of axon extension / axonal growth cone / monoatomic cation channel activity / calcium channel activity / melanosome / lamellipodium / cell body / positive regulation of cold-induced thermogenesis / axon / negative regulation of cell population proliferation / 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: 4 Å | ||||||
Authors | Dosey, T.L. / Wang, Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Structures of TRPV2 in distinct conformations provide insight into role of the pore turret. Authors: Timothy L Dosey / Zhao Wang / Guizhen Fan / Zhixian Zhang / Irina I Serysheva / Wah Chiu / Theodore G Wensel / Abstract: Cation channels of the transient receptor potential (TRP) family serve important physiological roles by opening in response to diverse intra- and extracellular stimuli that regulate their lower or ...Cation channels of the transient receptor potential (TRP) family serve important physiological roles by opening in response to diverse intra- and extracellular stimuli that regulate their lower or upper gates. Despite extensive studies, the mechanism coupling these gates has remained obscure. Previous structures have failed to resolve extracellular loops, known in the TRPV subfamily as 'pore turrets', which are proximal to the upper gates. We established the importance of the pore turret through activity assays and by solving structures of rat TRPV2, both with and without an intact turret at resolutions of 4.0 Å and 3.6 Å, respectively. These structures resolve the full-length pore turret and reveal fully open and partially open states of TRPV2, both with unoccupied vanilloid pockets. Our results suggest a mechanism by which physiological signals, such as lipid binding, can regulate the lower gate and couple to the upper gate through a pore-turret-facilitated mechanism. | ||||||
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 | 6bo4.cif.gz | 422.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bo4.ent.gz | 336.2 KB | Display | PDB format |
PDBx/mmJSON format | 6bo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/6bo4 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/6bo4 | HTTPS FTP |
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-Related structure data
Related structure data | 7118MC 7119C 6bo5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10247 (Title: TRPV2 ion channel gating through allosteric domain coupling revealed by cryo-EM Data size: 3.6 TB Data #1: TRPV2 WT with pore turret domain [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 79999.422 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 |
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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 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: .320 MDa / Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5457 / Plasmid: pYEPM |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 298 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Average exposure time: 10 sec. / Electron dose: 63 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 494689 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11789 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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