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Yorodumi- PDB-3j5p: Structure of TRPV1 ion channel determined by single particle elec... -
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-Basic information
Entry | Database: PDB / ID: 3j5p | ||||||
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Title | Structure of TRPV1 ion channel determined by single particle electron cryo-microscopy | ||||||
Components | Transient receptor potential cation channel subfamily V member 1 | ||||||
Keywords | TRANSPORT PROTEIN / TRPV1 channel | ||||||
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 / cellular response to temperature stimulus / TRP channels ...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 / cellular response to temperature stimulus / TRP channels / cellular response to acidic pH / fever generation / detection of temperature stimulus involved in thermoception / thermoception / negative regulation of systemic arterial blood pressure / glutamate secretion / chloride channel regulator activity / response to pH / dendritic spine membrane / monoatomic cation transmembrane transporter activity / excitatory extracellular ligand-gated monoatomic ion channel 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 / behavioral response to pain / diet induced thermogenesis / cellular response to cytokine stimulus / intracellularly gated calcium channel activity / 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 / GABA-ergic synapse / sensory perception of pain / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / calcium ion transmembrane transport / phosphoprotein binding / microglial cell activation / calcium channel activity / lipid metabolic process / cellular response to growth factor stimulus / response to peptide hormone / calcium ion transport / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / monoatomic ion transmembrane transport / cellular response to tumor necrosis factor / cellular response to heat / positive regulation of cytosolic calcium ion concentration / 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 | Liao, M. / Cao, E. / Julius, D. / Cheng, Y. | ||||||
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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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j5p.cif.gz | 416.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j5p.ent.gz | 337.5 KB | Display | PDB format |
PDBx/mmJSON format | 3j5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j5p_validation.pdf.gz | 921.1 KB | Display | wwPDB validaton report |
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Full document | 3j5p_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3j5p_validation.xml.gz | 100.3 KB | Display | |
Data in CIF | 3j5p_validation.cif.gz | 144 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/3j5p ftp://data.pdbj.org/pub/pdb/validation_reports/j5/3j5p | HTTPS FTP |
-Related structure data
Related structure data | 5778MC M: map data used to model this data C: citing same article (ref.) |
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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: 68242.156 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 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 / 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: K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods. |
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: 946 |
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: 3.275 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35645 / 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. (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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