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Yorodumi- PDB-6oo7: Cryo-EM structure of the C2-symmetric TRPV2/RTx complex in nanodiscs -
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-Basic information
Entry | Database: PDB / ID: 6oo7 | |||||||||
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Title | Cryo-EM structure of the C2-symmetric TRPV2/RTx complex in nanodiscs | |||||||||
Components | TRPV2 | |||||||||
Keywords | METAL TRANSPORT / ion channel / calcium channel / TRP channel | |||||||||
Function / homology | Function and homology information growth cone membrane / response to temperature stimulus / positive regulation of calcium ion import / calcium ion import across plasma membrane / positive regulation of axon extension / axonal growth cone / calcium channel activity / positive regulation of cold-induced thermogenesis / cell body / cell surface / identical protein binding Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Zubcevic, L. / Hsu, A.L. / Borgnia, M.J. / Lee, S.-Y. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2019 Title: Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes. Authors: Lejla Zubcevic / Allen L Hsu / Mario J Borgnia / Seok-Yong Lee / Abstract: The Transient Receptor Potential Vanilloid 2 (TRPV2) channel is a member of the temperature-sensing thermoTRPV family. Recent advances in cryo-electronmicroscopy (cryo-EM) and X-ray crystallography ...The Transient Receptor Potential Vanilloid 2 (TRPV2) channel is a member of the temperature-sensing thermoTRPV family. Recent advances in cryo-electronmicroscopy (cryo-EM) and X-ray crystallography have provided many important insights into the gating mechanisms of thermoTRPV channels. Interestingly, crystallographic studies of ligand-dependent TRPV2 gating have shown that the TRPV2 channel adopts two-fold symmetric arrangements during the gating cycle. However, it was unclear if crystal packing forces played a role in stabilizing the two-fold symmetric arrangement of the channel. Here, we employ cryo-EM to elucidate the structure of full-length rabbit TRPV2 in complex with the agonist resiniferatoxin (RTx) in nanodiscs and amphipol. We show that RTx induces two-fold symmetric conformations of TRPV2 in both environments. However, the two-fold symmetry is more pronounced in the native-like lipid environment of the nanodiscs. Our data offers insights into a gating pathway in TRPV2 involving symmetry transitions. | |||||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6oo7.cif.gz | 401.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oo7.ent.gz | 312.5 KB | Display | PDB format |
PDBx/mmJSON format | 6oo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oo7_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6oo7_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6oo7_validation.xml.gz | 71.7 KB | Display | |
Data in CIF | 6oo7_validation.cif.gz | 109.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/6oo7 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/6oo7 | HTTPS FTP |
-Related structure data
Related structure data | 20148MC 6oo3C 6oo4C 6oo5C 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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1 |
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-Components
#1: Protein | Mass: 88722.680 Da / Num. of mol.: 4 / Mutation: F470S, L505M, L508T, Q528E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: TRPV2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G1SNM3 #2: Chemical | ChemComp-6EU / |
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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 Details: TRPV2 in complex with RTx reconstituted into nanodiscs Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.300 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9 | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: TRPV2 in complex with RTx reconstituted into nanodiscs, monodisperse | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 296 K / Details: Blotted 3 seconds before plunging |
-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: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2254 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | |||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112622 / Num. of class averages: 2 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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