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Yorodumi- PDB-6l93: X-ray structure of the ligand-free human TRPV1 ankyrin repeat domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l93 | ||||||
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Title | X-ray structure of the ligand-free human TRPV1 ankyrin repeat domain | ||||||
Components | Transient receptor potential cation channel subfamily V member 1TRPV1 | ||||||
Keywords | TRANSPORT PROTEIN / Channel domain | ||||||
Function / homology | Function and homology information chemosensory behavior / temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / 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 ...chemosensory behavior / temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / 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 / thermoception / fever generation / detection of temperature stimulus involved in thermoception / glutamate secretion / dendritic spine membrane / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / TRP channels / cellular response to ATP / negative regulation of heart rate / cellular response to alkaloid / diet induced thermogenesis / behavioral response to pain / extracellular ligand-gated monoatomic ion channel activity / intracellularly gated calcium channel activity / negative regulation of mitochondrial membrane potential / detection of temperature stimulus involved in sensory perception of pain / 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 / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / cellular response to heat / cellular response to tumor necrosis factor / 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 / membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.47 Å | ||||||
Authors | Tanaka, M. / Hayakawa, K. / Unno, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l93.cif.gz | 341.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l93.ent.gz | 241.4 KB | Display | PDB format |
PDBx/mmJSON format | 6l93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/6l93 ftp://data.pdbj.org/pub/pdb/validation_reports/l9/6l93 | HTTPS FTP |
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-Related structure data
Related structure data | 2pnnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Homo sapiens (human) / Gene: TRPV1, VR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NER1 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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