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- PDB-3j5r: Reconstruction of TRPV1 ion channel in complex with capsaicin by ... -

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Entry
Database: PDB / ID: 3j5r
TitleReconstruction of TRPV1 ion channel in complex with capsaicin by single particle cryo-microscopy
ComponentsTransient receptor potential cation channel subfamily V member 1
KeywordsTRANSPORT PROTEIN / TRPV1 channel / capsaicin
Function / homology
Function and homology information


negative regulation of iodide transmembrane transport / positive regulation of membrane depolarization / negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / positive regulation of sensory perception of pain / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain ...negative regulation of iodide transmembrane transport / positive regulation of membrane depolarization / negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / positive regulation of sensory perception of pain / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / positive regulation of renal sodium excretion / negative regulation of axon regeneration / TRP channels / positive regulation of cardiac muscle cell differentiation / smooth muscle contraction involved in micturition / fever generation / detection of temperature stimulus involved in thermoception / thermoception / urinary bladder smooth muscle contraction / response to pH / monoatomic cation transmembrane transporter activity / glutamate secretion / negative regulation of systemic arterial blood pressure / dendritic spine membrane / positive regulation of urine volume / excitatory extracellular ligand-gated monoatomic ion channel activity / negative regulation of heart rate / response to acidic pH / response to pain / diet induced thermogenesis / cellular response to alkaloid / cellular response to cytokine stimulus / temperature homeostasis / cellular response to ATP / intracellularly gated calcium channel activity / detection of temperature stimulus involved in sensory perception of pain / negative regulation of mitochondrial membrane potential / behavioral response to pain / calcium ion import across plasma membrane / positive regulation of vasoconstriction / monoatomic ion channel activity / ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / cellular response to acidic pH / extracellular ligand-gated monoatomic ion channel activity / phosphatidylinositol binding / sensory perception of pain / axon terminus / positive regulation of excitatory postsynaptic potential / sarcoplasmic reticulum / lipid metabolic process / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / response to peptide hormone / cellular response to growth factor stimulus / GABA-ergic synapse / cellular response to tumor necrosis factor / calcium ion transmembrane transport / calcium channel activity / positive regulation of nitric oxide biosynthetic process / calcium ion transport / transmembrane signaling receptor activity / cellular response to heat / sensory perception of taste / response to heat / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / protein homotetramerization / calmodulin binding / postsynaptic membrane / 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 / membrane / metal ion binding / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily V member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLiao, M. / Cao, E. / Julius, D. / Cheng, Y.
CitationJournal: 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
DepositionOct 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
B: Transient receptor potential cation channel subfamily V member 1
A: Transient receptor potential cation channel subfamily V member 1
C: Transient receptor potential cation channel subfamily V member 1
D: Transient receptor potential cation channel subfamily V member 1


Theoretical massNumber of molelcules
Total (without water)272,9694
Polymers272,9694
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Transient receptor potential cation channel subfamily V member 1 / TrpV1 / Capsaicin receptor / Osm-9-like TRP channel 1 / OTRPC1 / Vanilloid receptor 1 / Vanilloid ...TrpV1 / Capsaicin receptor / Osm-9-like TRP channel 1 / OTRPC1 / Vanilloid receptor 1 / Vanilloid receptor type 1-like


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 detailsTHE 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 COORDINATES) WHOSE IDENTITIES ARE NOT KNOWN.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rat TRPV1 in complex with capsaicin / Type: COMPLEX / Details: tetramer
Molecular weightValue: 0.3 MDa / Experimental value: NO
Buffer solutionName: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP / pH: 7.4 / Details: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh Quantifoil grid
VitrificationInstrument: 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

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Jan 1, 2013
Details: Gatan K2 Summit operated in super-resolution counting mode, image recorded with dose fractionation method.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderSpecimen holder model: OTHER / Specimen holder type: FEI Polara cartridge
Image recordingElectron dose: 21 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Details: Operated in super-resolution counting mode, dose fractionation
Image scansNum. digital images: 900
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionMethod: Maximum likelihood / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33238 / 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 buildingProtocol: 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 stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms17564 0 0 0 17564

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