|Entry||Database: EMDB / ID: 5776|
|Title||Structure of the capsaicin receptor, TRPV1, in complex with DkTx and RTX determined by single particle electron cryo-microscopy|
|Map data||Reconstruction of rat TRPV1 channel in complex with DkTx and RTX|
|Sample||Rat TRPV1 in complex with DkTx and resiniferatoxin:|
|Keywords||TRPV1 channel / DkTx / RTX|
|Function / homology||Ankyrin repeat-containing domain / Ankyrin repeat profile. / Transient receptor potential channel, vanilloid 1-4 / Ion transport domain / in:ipr004729: / Ankyrin repeat / Transient receptor potential cation channel subfamily V member 1 / Transient receptor potential cation channel subfamily V / Ion transport protein / Ankyrin repeats (3 copies) ...Ankyrin repeat-containing domain / Ankyrin repeat profile. / Transient receptor potential channel, vanilloid 1-4 / Ion transport domain / in:ipr004729: / Ankyrin repeat / Transient receptor potential cation channel subfamily V member 1 / Transient receptor potential cation channel subfamily V / Ion transport protein / Ankyrin repeats (3 copies) / Ankyrin repeat-containing domain superfamily / Ankyrin repeat region circular profile. / TRP channels / detection of temperature stimulus involved in thermoception / peptide secretion / temperature-gated ion channel activity / response to capsazepine / sensory perception of mechanical stimulus / positive regulation of gastric acid secretion / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / dendritic spine membrane / 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
|Source||Rattus norvegicus (Norway rat)|
|Method||single particle reconstruction / cryo EM / 3.8 Å resolution|
|Authors||Liao M / Cao E / Julius D / Cheng Y|
|Citation||Journal: Nature / Year: 2013|
Title: TRPV1 structures in distinct conformations reveal activation mechanisms.
Authors: Erhu Cao / Maofu Liao / Yifan Cheng / David Julius
|Validation Report||PDB-ID: 3j5q|
SummaryFull reportAbout validation report
|Date||Deposition: Oct 24, 2013 / Header (metadata) release: Dec 4, 2013 / Map release: Dec 4, 2013 / Last update: Dec 18, 2013|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5776.map.gz (map file in CCP4 format, 65537 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.2156 Å|
CCP4 map header:
-Entire Rat TRPV1 in complex with DkTx and resiniferatoxin
|Entire||Name: Rat TRPV1 in complex with DkTx and resiniferatoxin / Details: The sample was monodisperse / Number of components: 1 / Oligomeric State: tetramer|
|Mass||Theoretical: 300 kDa / Experimental: 300 kDa|
-Component #1: protein, TRPV1
|Protein||Name: TRPV1 / Oligomeric Details: Tetramer|
Details: Functional minimal construct containing residues 110-603 and 627-764.
Recombinant expression: Yes / Number of Copies: 1
|Mass||Theoretical: 300 kDa / Experimental: 300 kDa|
|Source||Species: Rattus norvegicus (Norway rat)|
|Source (engineered)||Expression System: Homo sapiens (human) / Vector: pFastBac1 / Cell of expression system: HEK293S GnTI|
|Source (natural)||Location in cell: Plasma membrane|
|External references||UniProt: Transient receptor potential cation channel subfamily V member 1|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.3 mg/ml / Buffer solution: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP / pH: 7.4|
|Support film||400 mesh Quantifoil grid|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 90 % / Method: Blot for 6 sec|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300 / Date: Jan 1, 2013|
Details: Gatan K2 Summit operated in super-resolution counting mode; image recorded with dose fractionation method.
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 21 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 31000 X (nominal), 31000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3000 nm|
|Specimen Holder||Holder: Cooled to Liquid Nitrogen temperature / Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 900|
Details: Every image is the average of 30 frames recorded using the K2 Summit. The final reconstruction was calculated from images averaged from frames #3-#16.
|Processing||Method: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 36158|
Details: 3D classification, refinement, and reconstruction were performed using RELION.
|3D reconstruction||Algorithm: Maximum likelihood / Software: RELION / CTF correction: Each particle / Resolution: 3.8 Å / Resolution method: Gold standard FSC at 0.143 cut-off|
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