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Yorodumi- PDB-3j5q: Structure of TRPV1 ion channel in complex with DkTx and RTX deter... -
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-Basic information
Entry | Database: PDB / ID: 3j5q | |||||||||
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Title | Structure of TRPV1 ion channel in complex with DkTx and RTX determined by single particle electron cryo-microscopy | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN/TOXIN / TRPV1 channel / DkTx / RTX / TRANSPORT PROTEIN-TOXIN complex | |||||||||
Function / homology | Function and homology information temperature-gated ion channel activity / response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / urinary bladder smooth muscle contraction / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / TRP channels / cellular response to temperature stimulus ...temperature-gated ion channel activity / response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / urinary bladder smooth muscle contraction / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / TRP channels / cellular response to temperature stimulus / cellular response to acidic pH / excitatory extracellular ligand-gated monoatomic ion channel activity / fever generation / thermoception / detection of temperature stimulus involved in thermoception / glutamate secretion / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / dendritic spine membrane / response to pH / monoatomic cation transmembrane transporter activity / cellular response to ATP / ion channel inhibitor activity / negative regulation of heart rate / temperature homeostasis / response to pain / cellular response to alkaloid / calcium ion import across plasma membrane / diet induced thermogenesis / behavioral response to pain / intracellularly gated calcium channel activity / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / negative regulation of mitochondrial membrane potential / ligand-gated monoatomic ion channel activity / potassium channel regulator activity / sodium channel regulator activity / extracellular ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / monoatomic ion transmembrane transport / sensory perception of pain / : / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / lipid metabolic process / phosphoprotein binding / calcium ion transmembrane transport / microglial cell activation / calcium channel activity / transmembrane signaling receptor activity / cellular response to growth factor stimulus / response to peptide hormone / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / cellular response to heat / response to heat / postsynaptic membrane / protein homotetramerization / toxin activity / calmodulin binding / neuron projection / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / dendrite / negative regulation of transcription by RNA polymerase II / extracellular region / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) Chilobrachys guangxiensis (spider) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Liao, M. / Cao, E. / Julius, D. / Cheng, Y. | |||||||||
Citation | Journal: Nature / Year: 2013 Title: TRPV1 structures in distinct conformations reveal activation mechanisms. Authors: Erhu Cao / Maofu Liao / Yifan Cheng / David Julius / Abstract: Transient receptor potential (TRP) channels are polymodal signal detectors that respond to a wide range of physical and chemical stimuli. Elucidating how these channels integrate and convert ...Transient receptor potential (TRP) channels are polymodal signal detectors that respond to a wide range of physical and chemical stimuli. Elucidating how these channels integrate and convert physiological signals into channel opening is essential to understanding how they regulate cell excitability under normal and pathophysiological conditions. Here we exploit pharmacological probes (a peptide toxin and small vanilloid agonists) to determine structures of two activated states of the capsaicin receptor, TRPV1. A domain (consisting of transmembrane segments 1-4) that moves during activation of voltage-gated channels remains stationary in TRPV1, highlighting differences in gating mechanisms for these structurally related channel superfamilies. TRPV1 opening is associated with major structural rearrangements in the outer pore, including the pore helix and selectivity filter, as well as pronounced dilation of a hydrophobic constriction at the lower gate, suggesting a dual gating mechanism. Allosteric coupling between upper and lower gates may account for rich physiological modulation exhibited by TRPV1 and other TRP channels. | |||||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j5q.cif.gz | 432.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j5q.ent.gz | 339 KB | Display | PDB format |
PDBx/mmJSON format | 3j5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j5q_validation.pdf.gz | 949.1 KB | Display | wwPDB validaton report |
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Full document | 3j5q_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3j5q_validation.xml.gz | 111.5 KB | Display | |
Data in CIF | 3j5q_validation.cif.gz | 159.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/3j5q ftp://data.pdbj.org/pub/pdb/validation_reports/j5/3j5q | HTTPS FTP |
-Related structure data
Related structure data | 5776MC 5777C 3j5rC 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: 70795.211 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpv1, Vr1, Vr1l / Plasmid: pFastBac1 / Cell line (production host): HEK293S GnTI / Production host: Homo sapiens (human) / References: UniProt: O35433 #2: Protein/peptide | Mass: 3433.014 Da / Num. of mol.: 4 / Fragment: UNP residues 51-81 / Source method: isolated from a natural source / Source: (natural) Chilobrachys guangxiensis (spider) / References: UniProt: P0C247 Sequence details | THE TRPV1 CONSTRUCT COMPRISES RESIDUES 110-603 AND 627-764, WITH RESIDUES 604-626 DELETED. RESIDUES ...THE TRPV1 CONSTRUCT COMPRISES RESIDUES 110-603 AND 627-764, WITH RESIDUES 604-626 DELETED. RESIDUES 719-764 ARE NOT MODELED, WITH THE EXCEPTION OF 11 RESIDUES (NUMBERED 752-762 IN THE COORDINATE | |
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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: Rat TRPV1 in complex with DkTx and resiniferatoxin / Type: COMPLEX / Details: Tetramer |
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Molecular weight | Value: 0.3 MDa / Experimental value: NO |
Buffer solution | Name: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP / pH: 7.4 / Details: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 400 mesh Quantifoil grid |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temp: 120 K / Humidity: 90 % Details: Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III) Method: Blot for 6 sec |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Jan 1, 2013 Details: Gatan K2 Summit operated in super-resolution counting mode, image recorded with dose fractionation method. |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 31000 X / Calibrated magnification: 31000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / Camera length: 0 mm |
Specimen holder | Specimen holder model: OTHER / Specimen holder type: FEI Polara cartridge |
Image recording | Electron dose: 21 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) Details: Operated in super-resolution counting mode, dose fractionation |
Image scans | Num. digital images: 900 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software | Name: RELION / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: Each particle | ||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||
3D reconstruction | Method: Maximum likelihood / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36158 / Nominal pixel size: 1.2156 Å / Actual pixel size: 1.2156 Å Details: The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are included but are not well defined by the experimental ...Details: The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are included but are not well defined by the experimental density. Interatomic clashes between the ankyrin repeats and the C-terminal beta sheet are the result of poor geometry due to relatively poor experimental density in these regions. Resolution and averaging of DkTx density was insufficient to provide side chain geometry. The DkTx model was generated as a poly-ALA model based on hanatoxin (PDB entry 1D1H) and docked into the DkTx density with slight modification. (Single particle details: 3D classification, refinement, and reconstruction were performed using RELION) (Single particle--Applied symmetry: C4) Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL Details: REFINEMENT PROTOCOL--de novo model building DETAILS--The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are ...Details: REFINEMENT PROTOCOL--de novo model building DETAILS--The entire ankyrin structure was fitted as a single rigid body. As a result, the first two ankyrin repeats (UNP residues 111-199) are included but are not well defined by the experimental density. | ||||||||||||
Refinement step | Cycle: LAST
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