|Entry||Database: EMDB / ID: 5778|
|Title||Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy|
|Map data||Structure of the capsaicin receptor, TRPV1. This map is direct output from RELION without sharpening using a negative temperature factor. The map was normalized using the program MAPMAN.|
|Function / homology||Ankyrin repeat-containing domain / Ion transport protein / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / TRP channels / Transient receptor potential channel / Ankyrin repeats (3 copies) / Transient receptor potential cation channel subfamily V / Ankyrin repeat-containing domain superfamily ...Ankyrin repeat-containing domain / Ion transport protein / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / TRP channels / Transient receptor potential channel / Ankyrin repeats (3 copies) / Transient receptor potential cation channel subfamily V / Ankyrin repeat-containing domain superfamily / Ion transport domain / Transient receptor potential channel, vanilloid 1-4 / Transient receptor potential cation channel subfamily V member 1 / response to capsazepine / peptide secretion / detection of temperature stimulus involved in thermoception / temperature-gated ion channel activity / sensory perception of mechanical stimulus / positive regulation of gastric acid secretion / thermoception / detection of chemical stimulus involved in sensory perception of pain / dendritic spine membrane / negative regulation of establishment of blood-brain barrier / smooth muscle contraction involved in micturition / excitatory extracellular ligand-gated ion channel activity / urinary bladder smooth muscle contraction / cellular response to temperature stimulus / diet induced thermogenesis / calcium ion import across plasma membrane / cellular response to acidic pH / fever generation / chloride channel regulator activity / temperature homeostasis / cation transmembrane transporter activity / behavioral response to pain / glutamate secretion / detection of temperature stimulus involved in sensory perception of pain / cation channel activity / calcium-release channel activity / intrinsic component of plasma membrane / response to pain / cellular response to ATP / cellular response to alkaloid / ligand-gated ion channel activity / extracellular ligand-gated ion channel activity / phosphatidylinositol binding / microglial cell activation / calcium channel activity / calcium ion transmembrane transport / cellular response to cytokine stimulus / sensory perception of pain / cellular response to nerve growth factor stimulus / response to organonitrogen compound / response to peptide hormone / calcium ion transport / lipid metabolic process / ion transmembrane transport / cellular response to growth factor stimulus / phosphoprotein binding / cellular response to heat / 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 / ion channel activity / calmodulin binding / neuron projection / synapse / cell junction / dendrite / neuronal cell body / external side of plasma membrane / inflammatory response / positive regulation of apoptotic process / 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 / 3.275 Å resolution|
|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.
|Validation Report||PDB-ID: 3j5p|
About validation report
|Date||Deposition: Oct 24, 2013 / Header (metadata) release: Dec 4, 2013 / Map release: Dec 4, 2013 / Last update: Oct 14, 2015|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5778.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
|Entire||Name: Rat TRPV1 / 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: UniProt:O35433|
|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 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 / 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: 946|
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.
URL of raw data: http://dx.doi.org/10.6019/EMPIAR-10005
|Raw data||EMPIAR-10005 (Title: TRPV1 dataset taken on a K2 direct electron detector / Data size: 6.3 TB|
Data #1: TRPV1 picked particles [picked particles - multiframe - processed]
Data #2: TRPV1 raw multi-frame micrographs [micrographs - multiframe]
Data #3: TRPV1 summed frame micrographs [micrographs - single frame])
|Processing||Method: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 35645|
Details: 3D classification, refinement, and reconstruction were performed using RELION.
|3D reconstruction||Algorithm: Maximum likelihood / Software: RELION / CTF correction: Each particle / Resolution: 3.275 Å / Resolution method: Gold standard FSC at 0.143 cut-off|
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