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Yorodumi- PDB-3j9j: Structure of the capsaicin receptor, TRPV1, determined by single ... -
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-Basic information
Entry | Database: PDB / ID: 3j9j | ||||||
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Title | Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy | ||||||
Components | Transient receptor potential cation channel subfamily V member 1 | ||||||
Keywords | MEMBRANE PROTEIN / alpha helical | ||||||
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 / 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 / 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 / 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 / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.275 Å | ||||||
Authors | Wang, R.Y.-R. / Barad, B.A. / Fraser, J.S. / DiMaio, F. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Authors: Maofu Liao / Erhu Cao / David Julius / Yifan Cheng / Abstract: Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been ...Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4 Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane segments 5-6 (S5-S6) and the intervening pore loop, which is flanked by S1-S4 voltage-sensor-like domains. TRPV1 has a wide extracellular 'mouth' with a short selectivity filter. The conserved 'TRP domain' interacts with the S4-S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including amino-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function. | ||||||
History |
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Remark 0 | THIS ENTRY 3J9J CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-5778) DETERMINED ...THIS ENTRY 3J9J CONTAINS A STRUCTURAL MODEL FIT TO AN ELECTRON MICROSCOPY MAP (EMD-5778) DETERMINED ORIGINALLY BY AUTHORS: M.LIAO, E.CAO, D.JULIUS, Y.CHENG |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j9j.cif.gz | 440.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j9j.ent.gz | 349.6 KB | Display | PDB format |
PDBx/mmJSON format | 3j9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j9j_validation.pdf.gz | 937.4 KB | Display | wwPDB validaton report |
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Full document | 3j9j_full_validation.pdf.gz | 943.3 KB | Display | |
Data in XML | 3j9j_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 3j9j_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/3j9j ftp://data.pdbj.org/pub/pdb/validation_reports/j9/3j9j | HTTPS FTP |
-Related structure data
Related structure data | 5778M M: map data used to model this data |
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Similar structure data | |
EM raw data | EMPIAR-10005 (Title: TRPV1 dataset taken on a K2 direct electron detector / Data size: 6.3 TB / Data #1: TRPV1 picked particles [tilt series] Data #2: TRPV1 raw multi-frame micrographs [micrographs - multiframe] Data #3: TRPV1 summed frame micrographs [micrographs - single frame]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 67234.953 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: O35433 Sequence details | PROTEIN CONSTRUCT COMPRISES UNP RESIDUES 111-603 AND 627-719. | |
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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 / Type: COMPLEX |
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Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE |
-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 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 31000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 21 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
-Processing
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||
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3D reconstruction | Resolution: 3.275 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35645 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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