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- EMDB-40940: TRPV1 in Nanodisc bound with lysophosphatidic acid in all four mo... -
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Open data
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Basic information
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Title | TRPV1 in Nanodisc bound with lysophosphatidic acid in all four monomers | |||||||||
![]() | TRPV1 in nanodisc bound with LPA in all four monomers. | |||||||||
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![]() | TRPV1 / lysophosphatidic acid / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() temperature-gated ion channel activity / response to capsazepine / 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 ...temperature-gated ion channel activity / response to capsazepine / 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 / excitatory extracellular ligand-gated monoatomic ion channel activity / thermoception / fever generation / detection of temperature stimulus involved in thermoception / glutamate secretion / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / response to pH / dendritic spine membrane / monoatomic cation transmembrane transporter activity / extracellular ligand-gated monoatomic ion channel activity / cellular response to ATP / negative regulation of heart rate / temperature homeostasis / response to pain / cellular response to alkaloid / behavioral response to pain / diet induced thermogenesis / intracellularly gated calcium channel activity / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / negative regulation of mitochondrial membrane potential / ligand-gated monoatomic ion channel activity / calcium ion import across plasma membrane / monoatomic cation channel activity / monoatomic ion transmembrane transport / sensory perception of pain / response to organonitrogen compound / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / calcium ion transmembrane transport / phosphoprotein binding / microglial cell activation / calcium channel activity / lipid metabolic process / cellular response to growth factor stimulus / response to peptide hormone / transmembrane signaling receptor activity / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cellular response to tumor necrosis factor / cellular response to heat / 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 / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Arnold WR / Cheng Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of TRPV1 modulation by endogenous bioactive lipids. Authors: William R Arnold / Adamo Mancino / Frank R Moss / Adam Frost / David Julius / Yifan Cheng / ![]() Abstract: TRP ion channels are modulated by phosphoinositide lipids, but the underlying structural mechanisms remain unclear. The capsaicin- and heat-activated receptor, TRPV1, has served as a model for ...TRP ion channels are modulated by phosphoinositide lipids, but the underlying structural mechanisms remain unclear. The capsaicin- and heat-activated receptor, TRPV1, has served as a model for deciphering lipid modulation, which is relevant to understanding how pro-algesic agents enhance channel activity in the setting of inflammatory pain. Identification of a pocket within the TRPV1 transmembrane core has provided initial clues as to how phosphoinositide lipids bind to and regulate the channel. Here we show that this regulatory pocket in rat TRPV1 can accommodate diverse lipid species, including the inflammatory lipid lysophosphatidic acid, whose actions are determined by their specific modes of binding. Furthermore, we show that an empty-pocket channel lacking an endogenous phosphoinositide lipid assumes an agonist-like state, even at low temperature, substantiating the concept that phosphoinositide lipids serve as negative TRPV1 modulators whose ejection from the binding pocket is a critical step toward activation by thermal or chemical stimuli. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 202.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.9 KB 14.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.3 KB | Display | ![]() |
Images | ![]() | 58.9 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 200.3 MB 200.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 993.1 KB | Display | ![]() |
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Full document | ![]() | 992.6 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t0cMC ![]() 8t0eC ![]() 8t0yC ![]() 8t10C ![]() 8t3lC ![]() 8t3mC ![]() 8u2zC ![]() 8u30C ![]() 8u3aC ![]() 8u3cC ![]() 8u3jC ![]() 8u3lC ![]() 8u43C ![]() 8u4dC 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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Annotation | TRPV1 in nanodisc bound with LPA in all four monomers. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map A for TRPV1 in nanodisc bound with LPA in all four monomers.
File | emd_40940_half_map_1.map | ||||||||||||
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Annotation | Half Map A for TRPV1 in nanodisc bound with LPA in all four monomers. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B for TRPV1 in nanodisc bound with LPA in all four monomers.
File | emd_40940_half_map_2.map | ||||||||||||
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Annotation | Half Map B for TRPV1 in nanodisc bound with LPA in all four monomers. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : TRPV1 in nanodisc bound with lysophosphatidic acid in all four mo...
Entire | Name: TRPV1 in nanodisc bound with lysophosphatidic acid in all four monomers |
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Components |
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-Supramolecule #1: TRPV1 in nanodisc bound with lysophosphatidic acid in all four mo...
Supramolecule | Name: TRPV1 in nanodisc bound with lysophosphatidic acid in all four monomers type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 688 KDa |
-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: 92.654172 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRLF GKGDSEEASP LDCPYEEGGL ASCPIITVSS VLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD AVAQSNCQEL ESLLPFLQRS KKRLTDSEFK DPETGKTCLL K AMLNLHNG ...String: MEQRASLDSE ESESPPQENS CLDPPDRDPN CKPPPVKPHI FTTRSRTRLF GKGDSEEASP LDCPYEEGGL ASCPIITVSS VLTIQRPGD GPASVRPSSQ DSVSAGEKPP RLYDRRSIFD AVAQSNCQEL ESLLPFLQRS KKRLTDSEFK DPETGKTCLL K AMLNLHNG QNDTIALLLD VARKTDSLKQ FVNASYTDSY YKGQTALHIA IERRNMTLVT LLVENGADVQ AAANGDFFKK TK GRPGFYF GELPLSLAAC TNQLAIVKFL LQNSWQPADI SARDSVGNTV LHALVEVADN TVDNTKFVTS MYNEILILGA KLH PTLKLE EITNRKGLTP LALAASSGKI GVLAYILQRE IHEPECRHLS RKFTEWAYGP VHSSLYDLSC IDTCEKNSVL EVIA YSSSE TPNRHDMLLV EPLNRLLQDK WDRFVKRIFY FNFFVYCLYM IIFTAAAYYR PVEGLPPYKL KNTVGDYFRV TGEIL SVSG GVYFFFRGIQ YFLQRRPSLK SLFVDSYSEI LFFVQSLFML VSVVLYFSQR KEYVASMVFS LAMGWTNMLY YTRGFQ QMG IYAVMIEKMI LRDLCRFMFV YLVFLFGFST AVVTLIEDGK YNSLYSTCLE LFKFTIGMGD LEFTENYDFK AVFIILL LA YVILTYILLL NMLIALMGET VNKIAQESKN IWKLQRAITI LDTEKSFLKC MRKAFRSGKL LQVGFTPDGK DDYRWCFR V DEVNWTTWNT NVGIINEDPG NCEGVKRTLS FSLRSGRVSG RNWKNFALVP LLRDASTRDR HATQQEEVQL KHYTGSLKP EDAEVFKDSM VPGEK UniProtKB: Transient receptor potential cation channel subfamily V member 1 |
-Macromolecule #2: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate
Macromolecule | Name: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate / type: ligand / ID: 2 / Number of copies: 4 / Formula: NKN |
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Molecular weight | Theoretical: 382.429 Da |
Chemical component information | ![]() ChemComp-NKN: |
-Macromolecule #3: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2 |
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Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |