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- PDB-6l93: X-ray structure of the ligand-free human TRPV1 ankyrin repeat domain -
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Open data
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Basic information
Entry | Database: PDB / ID: 6l93 | ||||||
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Title | X-ray structure of the ligand-free human TRPV1 ankyrin repeat domain | ||||||
![]() | Transient receptor potential cation channel subfamily V member 1 | ||||||
![]() | TRANSPORT PROTEIN / Channel domain | ||||||
Function / homology | ![]() chemosensory behavior / temperature-gated ion channel activity / response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / smooth muscle contraction involved in micturition / cellular response to acidic pH ...chemosensory behavior / temperature-gated ion channel activity / response to capsazepine / negative regulation of establishment of blood-brain barrier / sensory perception of mechanical stimulus / peptide secretion / detection of chemical stimulus involved in sensory perception of pain / cellular response to temperature stimulus / smooth muscle contraction involved in micturition / cellular response to acidic pH / excitatory extracellular ligand-gated monoatomic ion channel activity / thermoception / fever generation / detection of temperature stimulus involved in thermoception / glutamate secretion / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / dendritic spine membrane / TRP channels / extracellular ligand-gated monoatomic ion channel activity / cellular response to ATP / negative regulation of heart rate / cellular response to alkaloid / behavioral response to pain / diet induced thermogenesis / intracellularly gated calcium channel activity / detection of temperature stimulus involved in sensory perception of pain / negative regulation of mitochondrial membrane potential / calcium ion import across plasma membrane / voltage-gated calcium channel activity / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / calcium ion transmembrane transport / phosphoprotein binding / microglial cell activation / calcium channel activity / lipid metabolic process / response to peptide hormone / transmembrane signaling receptor activity / positive regulation of nitric oxide biosynthetic process / cellular response to tumor necrosis factor / cellular response to heat / positive regulation of cytosolic calcium ion concentration / postsynaptic membrane / protein homotetramerization / cell surface receptor signaling pathway / calmodulin binding / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / negative regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanaka, M. / Hayakawa, K. / Unno, M. | ||||||
![]() | ![]() Title: Structure determination of the human TRPV1 ankyrin-repeat domain under nonreducing conditions. Authors: Tanaka, M. / Hayakawa, K. / Ogawa, N. / Kurokawa, T. / Kitanishi, K. / Ite, K. / Matsui, T. / Mori, Y. / Unno, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 341.9 KB | Display | ![]() |
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PDB format | ![]() | 241.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.2 KB | Display | ![]() |
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Full document | ![]() | 489.8 KB | Display | |
Data in XML | ![]() | 50.7 KB | Display | |
Data in CIF | ![]() | 67.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pnnS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30833.143 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.46 Å3/Da / Density % sol: 72.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.125 M sodium citrate (pH 5.0), 5% PEG 8000, 2.5% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 4.47→32.95 Å / Num. obs: 19438 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 179.57 Å2 / CC1/2: 0.993 / Rsym value: 0.098 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 4.47→4.63 Å / Num. unique obs: 4678 / CC1/2: 0.817 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PNN Resolution: 4.47→32.95 Å / SU ML: 0.5466 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.6591 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 184.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.47→32.95 Å
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Refine LS restraints |
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LS refinement shell |
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