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- PDB-3j5q: Structure of TRPV1 ion channel in complex with DkTx and RTX deter... -

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Basic information

Entry
Database: PDB / ID: 3j5q
TitleStructure of TRPV1 ion channel in complex with DkTx and RTX determined by single particle electron cryo-microscopy
Components
  • Double-knot toxin
  • Transient receptor potential cation channel subfamily V member 1
KeywordsTRANSPORT PROTEIN/TOXIN / TRPV1 channel / DkTx / RTX / TRANSPORT PROTEIN-TOXIN complex
Function / homologyAnkyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat / in:ipr004729: / Transient receptor potential channel, vanilloid 1-4 / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Transient receptor potential cation channel subfamily V member 1 / Ankyrin repeat-containing domain superfamily / Ion transport protein ...Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat / in:ipr004729: / Transient receptor potential channel, vanilloid 1-4 / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V / Transient receptor potential cation channel subfamily V member 1 / Ankyrin repeat-containing domain superfamily / Ion transport protein / Ion transport domain / Ankyrin repeat profile. / TRP channels / Ankyrin repeat region circular profile. / response to capsazepine / peptide secretion / temperature-gated ion channel activity / detection of temperature stimulus involved in thermoception / sensory perception of mechanical stimulus / positive regulation of gastric acid secretion / detection of chemical stimulus involved in sensory perception of pain / dendritic spine membrane / smooth muscle contraction involved in micturition / negative regulation of establishment of blood-brain barrier / excitatory extracellular ligand-gated ion channel activity / diet induced thermogenesis / cellular response to acidic pH / cellular response to temperature stimulus / behavioral response to pain / calcium ion import across plasma membrane / fever generation / chloride channel regulator activity / cation transmembrane transporter activity / glutamate secretion / cation channel activity / detection of temperature stimulus involved in sensory perception of pain / ligand-gated ion channel activity / calcium-release channel activity / intrinsic component of plasma membrane / cellular response to ATP / cellular response to alkaloid / extracellular ligand-gated ion channel activity / phosphatidylinositol binding / microglial cell activation / calcium ion transmembrane transport / cellular response to cytokine stimulus / cellular response to growth factor stimulus / cellular response to nerve growth factor stimulus / calcium ion transport / response to peptide hormone / lipid metabolic process / cellular response to heat / phosphoprotein binding / response to pH / transmembrane signaling receptor activity / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / postsynaptic membrane / protein homotetramerization / response to heat / positive regulation of nitric oxide biosynthetic process / calmodulin binding / synapse / cell junction / external side of plasma membrane / inflammatory response / positive regulation of apoptotic process / dendrite / neuronal cell body / integral component of plasma membrane / negative regulation of transcription by RNA polymerase II / membrane / integral component of membrane / ATP binding / identical protein binding / plasma membrane / metal ion binding / cytosol / Transient receptor potential cation channel subfamily V member 1
Function and homology information
Specimen sourceRattus norvegicus (Norway rat)
Chilobrachys jingzhao (spider)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 28, 2013 / Release: Dec 4, 2013
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 4, 2013Structure modelrepositoryInitial release
1.1Dec 11, 2013Structure modelDatabase references
1.2Dec 18, 2013Structure modelDatabase references
1.3Jul 18, 2018Structure modelData collectionem_software_em_software.image_processing_id / _em_software.name

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Assembly

Deposited unit
D: Transient receptor potential cation channel subfamily V member 1
B: Transient receptor potential cation channel subfamily V member 1
E: Transient receptor potential cation channel subfamily V member 1
G: Transient receptor potential cation channel subfamily V member 1
A: Double-knot toxin
C: Double-knot toxin
F: Double-knot toxin
H: Double-knot toxin


Theoretical massNumber of molelcules
Total (without water)283,5948
Polyers283,5948
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide
Transient receptor potential cation channel subfamily V member 1 / 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: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpv1, Vr1, Vr1l / Plasmid name: pFastBac1 / Cell line (production host): HEK293S GnTI / Production host: Homo sapiens (human) / References: UniProt: O35433
#2: Protein/peptide
Double-knot toxin / DkTx


Mass: 2656.265 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999 / Source: (natural) Chilobrachys jingzhao (spider)
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. THE SEQUENCE REGISTER OF DKTX IS ALSO UNKNOWN, SO ALL DKTX RESIDUES HAVE BEEN MODELED AS UNK (UNKNOWN RESIDUE).

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Rat TRPV1 in complex with DkTx and resiniferatoxin / Type: COMPLEX / Details: Tetramer
Molecular weightValue: 0.3 MDa / Experimental value: NO
Buffer solutionName: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP / Details: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP / pH: 7.4
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
MicroscopyMicroscope model: 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 FIELDBright-field microscopy / Nominal magnification: 31000 / Calibrated magnification: 31000 / 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
Details: Operated in super-resolution counting mode, dose fractionation
Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNumber digital images: 900
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m 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
3D reconstructionMethod: Maximum likelihood / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 36158 / Nominal pixel size: 1.2156 / Actual pixel size: 1.2156
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. Interatomic clashes between the ankyrin repeats and the C-terminal beta sheet are the result of poor geometry due to relatively poor experimental density in these regions. Resolution and averaging of DkTx density was insufficient to provide side chain geometry. The DkTx model was generated as a poly-ALA model based on hanatoxin (PDB entry 1D1H) and docked into the DkTx density with slight modification. (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 buildingDetails: 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.
Ref protocol: AB INITIO MODEL / Ref space: REAL
Number of atoms included #LASTProtein: 18264 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 18264

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