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Yorodumi- PDB-5hi9: Structure of the full-length TRPV2 channel by cryo-electron microscopy -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hi9 | ||||||
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Title | Structure of the full-length TRPV2 channel by cryo-electron microscopy | ||||||
Components | Transient Receptor Potential Cation Channel Subfamily V Member 2 | ||||||
Keywords | TRANSPORT PROTEIN / TRPV2 ion channel | ||||||
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 / positive regulation of cold-induced thermogenesis ...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 / 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: 4.4 Å | ||||||
Authors | Huynh, K.W. / Cohen, M.R. / Jiansen, J. / Samanta, A. / Lodowski, D.T. / Zhou, Z.H. / Moiseenkova-Bell, V.Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2016 Title: Structure of the full-length TRPV2 channel by cryo-EM. Authors: Kevin W Huynh / Matthew R Cohen / Jiansen Jiang / Amrita Samanta / David T Lodowski / Z Hong Zhou / Vera Y Moiseenkova-Bell / Abstract: Transient receptor potential (TRP) proteins form a superfamily Ca(2+)-permeable cation channels regulated by a range of chemical and physical stimuli. Structural analysis of a 'minimal' TRP vanilloid ...Transient receptor potential (TRP) proteins form a superfamily Ca(2+)-permeable cation channels regulated by a range of chemical and physical stimuli. Structural analysis of a 'minimal' TRP vanilloid subtype 1 (TRPV1) elucidated a mechanism of channel activation by agonists through changes in its outer pore region. Though homologous to TRPV1, other TRPV channels (TRPV2-6) are insensitive to TRPV1 activators including heat and vanilloids. To further understand the structural basis of TRPV channel function, we determined the structure of full-length TRPV2 at ∼5 Å resolution by cryo-electron microscopy. Like TRPV1, TRPV2 contains two constrictions, one each in the pore-forming upper and lower gates. The agonist-free full-length TRPV2 has wider upper and lower gates compared with closed and agonist-activated TRPV1. We propose these newly revealed TRPV2 structural features contribute to diversity of TRPV channels. | ||||||
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 | 5hi9.cif.gz | 440.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hi9.ent.gz | 364.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hi9_validation.pdf.gz | 938.2 KB | Display | wwPDB validaton report |
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Full document | 5hi9_full_validation.pdf.gz | 1015.2 KB | Display | |
Data in XML | 5hi9_validation.xml.gz | 80 KB | Display | |
Data in CIF | 5hi9_validation.cif.gz | 116.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/5hi9 ftp://data.pdbj.org/pub/pdb/validation_reports/hi/5hi9 | HTTPS FTP |
-Related structure data
Related structure data | 6580MC 6618MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 87667.789 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Details (production host): YepM Plasmid / Production host: Saccharomycetales (fungus) / Strain (production host): BJ5457 / 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: Transient Receptor Potential cation Channel Subfamily V Member 2 Type: COMPLEX / Details: Recombinant Purified Protein / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.340 MDa / Experimental value: YES |
Buffer solution | pH: 8 |
Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 15 % / Chamber temperature: 298 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 magnification: 31000 X |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 21 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 988 / Details: Gatan K2 Summit in super-resolution counting mode. |
-Processing
Software | Name: PHENIX / Version: dev_2247: / Classification: refinement | |||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | |||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42550 / Symmetry type: POINT | |||||||||||||||||||||||||
Refinement | Highest resolution: 4.4 Å | |||||||||||||||||||||||||
Refine LS restraints |
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