[English] 日本語
Yorodumi- EMDB-5777: Reconstruction of rat TRPV1 channel in complex with capsaicin by ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5777 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Reconstruction of rat TRPV1 channel in complex with capsaicin by single particle cryo-microscopy | |||||||||
Map data | Reconstruction of rat TRPV1 in complex with capsaicin | |||||||||
Sample |
| |||||||||
Keywords | TRPV1 channel / capsaicin | |||||||||
Function / homology | Function and homology information temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / 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 / cellular response to temperature stimulus / smooth muscle contraction involved in micturition ...temperature-gated ion channel activity / response to capsazepine / excitatory extracellular ligand-gated monoatomic ion channel activity / 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 / cellular response to temperature stimulus / smooth muscle contraction involved in micturition / TRP channels / cellular response to acidic pH / thermoception / fever generation / detection of temperature stimulus involved in thermoception / dendritic spine membrane / glutamate secretion / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / response to pH / monoatomic cation transmembrane transporter activity / cellular response to ATP / response to pain / temperature homeostasis / negative regulation of heart rate / detection of temperature stimulus involved in sensory perception of pain / cellular response to alkaloid / diet induced thermogenesis / extracellular ligand-gated monoatomic ion channel activity / behavioral response to pain / intracellularly gated calcium channel activity / cellular response to cytokine stimulus / negative regulation of mitochondrial membrane potential / calcium ion import across plasma membrane / ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / sensory perception of pain / response to organonitrogen compound / monoatomic ion transmembrane transport / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / calcium ion transmembrane transport / microglial cell activation / calcium channel activity / lipid metabolic process / response to peptide hormone / phosphoprotein binding / cellular response to growth factor stimulus / calcium ion transport / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / cellular response to heat / cellular response to tumor necrosis factor / 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 / membrane / metal ion binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
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 / 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5777.map.gz | 45.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-5777-v30.xml emd-5777.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_5777_1.jpg | 141.8 KB | ||
Others | TRPV1_capsaicin_sharpened_-200_4.2A.map | 64 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5777 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5777 | HTTPS FTP |
-Related structure data
Related structure data | 3j5rMC 5776C 3j5qC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_5777.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of rat TRPV1 in complex with capsaicin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2156 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Supplemental map: TRPV1 capsaicin sharpened -200 4.2A.map
File | TRPV1_capsaicin_sharpened_-200_4.2A.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Rat TRPV1 in complex with capsaicin
Entire | Name: Rat TRPV1 in complex with capsaicin |
---|---|
Components |
|
-Supramolecule #1000: Rat TRPV1 in complex with capsaicin
Supramolecule | Name: Rat TRPV1 in complex with capsaicin / type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: tetramer / Number unique components: 1 |
---|---|
Molecular weight | Experimental: 300 KDa / Theoretical: 300 KDa |
-Macromolecule #1: TRPV1
Macromolecule | Name: TRPV1 / type: protein_or_peptide / ID: 1 Details: Functional minimal construct containing residues 110-603 and 627-764. Number of copies: 1 / Oligomeric state: Tetramer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Rattus norvegicus (Norway rat) / synonym: Rat / Location in cell: Plasma membrane |
Molecular weight | Experimental: 300 KDa / Theoretical: 300 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293S GnTI / Recombinant plasmid: pFastBac1 |
Sequence | UniProtKB: Transient receptor potential cation channel subfamily V member 1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
---|---|
Buffer | pH: 7.4 / Details: 150 mM NaCl, 20 mM HEPES, 2 mM TCEP |
Grid | Details: 400 mesh Quantifoil grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 6 sec |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 31000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 31000 |
Sample stage | Specimen holder: Cooled to Liquid Nitrogen temperature / Specimen holder model: OTHER |
Details | Gatan K2 Summit operated in super-resolution counting mode; image recorded with dose fractionation method. |
Date | Jan 1, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 900 / Average electron dose: 21 e/Å2 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. |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
---|---|
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 33238 |
Details | 3D classification, refinement, and reconstruction were performed using RELION. |