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Open data
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Basic information
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Title | Structure of rat TRPV1 in complex with PSFL426-S5 | |||||||||
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![]() | TRPV1 / protein complex / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / TRP channels / smooth muscle contraction involved in micturition ...negative regulation of establishment of blood-brain barrier / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / cellular response to temperature stimulus / excitatory extracellular ligand-gated monoatomic ion channel activity / temperature-gated ion channel activity / detection of chemical stimulus involved in sensory perception of pain / TRP channels / smooth muscle contraction involved in micturition / fever generation / urinary bladder smooth muscle contraction / thermoception / detection of temperature stimulus involved in thermoception / cellular response to acidic pH / negative regulation of systemic arterial blood pressure / response to pH / chloride channel regulator activity / dendritic spine membrane / glutamate secretion / monoatomic cation transmembrane transporter activity / cellular response to ATP / negative regulation of heart rate / ligand-gated monoatomic ion channel activity / response to pain / cellular response to alkaloid / temperature homeostasis / diet induced thermogenesis / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / intracellularly gated calcium channel activity / behavioral response to pain / negative regulation of mitochondrial membrane potential / calcium ion import across plasma membrane / monoatomic cation channel activity / extracellular ligand-gated monoatomic ion channel activity / sensory perception of pain / phosphatidylinositol binding / phosphoprotein binding / microglial cell activation / cellular response to nerve growth factor stimulus / GABA-ergic synapse / calcium ion transmembrane transport / calcium channel activity / cellular response to growth factor stimulus / response to peptide hormone / lipid metabolic process / positive regulation of nitric oxide biosynthetic process / calcium ion transport / transmembrane signaling receptor activity / cellular response to tumor necrosis factor / sensory perception of taste / cellular response to heat / positive regulation of cytosolic calcium ion concentration / response to heat / monoatomic ion transmembrane transport / protein homotetramerization / postsynaptic membrane / 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 / metal ion binding / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Chen X / Yu Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of rat TRPV1 in complex with PSFL426-S5 Authors: Chen X / Yu Y | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15 KB 15 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 84.1 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 59.1 MB 59.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9isgMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.93 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_60835_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_60835_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Structure of rat TRPV1 in complex with PSFL426-S5
Entire | Name: Structure of rat TRPV1 in complex with PSFL426-S5 |
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Components |
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-Supramolecule #1: Structure of rat TRPV1 in complex with PSFL426-S5
Supramolecule | Name: Structure of rat TRPV1 in complex with PSFL426-S5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Transient receptor potential cation channel subfamily V member 1
Macromolecule | Name: Transient receptor potential cation channel subfamily V member 1 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 99.645812 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DMEQRASLDS EESESPPQEN SCLDPPDRDP NCKPPPVKPH IFTTRSRTR LFGKGDSEEA SPLDCPYEEG GLASCPIITV SSVLTIQRPG DGPASVRPSS QDSVSAGEKP PRLYDRRSIF D AVAQSNCQ ...String: MDYKDDDDKW SHPQFEKGGG GSGGSAWSHP QFEKEFKGLV DMEQRASLDS EESESPPQEN SCLDPPDRDP NCKPPPVKPH IFTTRSRTR LFGKGDSEEA SPLDCPYEEG GLASCPIITV SSVLTIQRPG DGPASVRPSS QDSVSAGEKP PRLYDRRSIF D AVAQSNCQ ELESLLPFLQ RSKKRLTDSE FKDPETGKTC LLKAMLNLHN GQNDTIALLL DVARKTDSLK QFVNASYTDS YY KGQTALH IAIERRNMTL VTLLVENGAD VQAAANGDFF KKTKGRPGFY FGELPLSLAA CTNQLAIVKF LLQNSWQPAD ISA RDSVGN TVLHALVEVA DNTVDNTKFV TSMYNEILIL GAKLHPTLKL EEITNRKGLT PLALAASSGK IGVLAYILQR EIHE PECRH LSRKFTEWAY GPVHSSLYDL SCIDTCEKNS VLEVIAYSSS ETPNRHDMLL VEPLNRLLQD KWDRFVKRIF YFNFF VYCL YMIIFTAAAY YRPVEGLPPY KLKNTVGDYF RVTGEILSVS GGVYFFFRGI QYFLQRRPSL KSLFVDSYSE ILFFVQ SLF MLVSVVLYFS QRKEYVASMV FSLAMGWTNM LYYTRGFQQM GIYAVMIEKM ILRDLCRFMF VYLVFLFGFS TAVVTLI ED GKNNSLPMES TPHKCRGSAC KPGNSYNSLY STCLELFKFT IGMGDLEFTE NYDFKAVFII LLLAYVILTY ILLLNMLI A LMGETVNKIA QESKNIWKLQ RAITILDTEK SFLKCMRKAF RSGKLLQVGF TPDGKDDYRW CFRVDEVNWT TWNTNVGII NEDPGNCEGV KRTLSFSLRS GRVSGRNWKN FALVPLLRDA STRDRHATQQ EEVQLKHYTG SLKPEDAEVF KDSMVPGEK UniProtKB: Transient receptor potential cation channel subfamily V member 1 |
-Macromolecule #2: 4-azanyl-3-sulfanylidene-1,2,4-triazine-5,6-dione
Macromolecule | Name: 4-azanyl-3-sulfanylidene-1,2,4-triazine-5,6-dione / type: ligand / ID: 2 / Number of copies: 4 / Formula: A1D92 |
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Molecular weight | Theoretical: 158.139 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 4.5 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |