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- EMDB-41855: TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer) -
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Open data
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Basic information
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Title | TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer) | |||||||||
![]() | TRPV1 monomer bound with PI-Br4 in Conformation 1 | |||||||||
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![]() | TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer) / 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 / smooth muscle contraction involved in micturition / TRP channels / cellular response to temperature stimulus ...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 / smooth muscle contraction involved in micturition / TRP channels / cellular response to temperature stimulus / cellular response to acidic pH / excitatory extracellular ligand-gated monoatomic ion channel activity / fever generation / thermoception / detection of temperature stimulus involved in thermoception / glutamate secretion / negative regulation of systemic arterial blood pressure / chloride channel regulator activity / dendritic spine membrane / response to pH / monoatomic cation transmembrane transporter activity / cellular response to ATP / negative regulation of heart rate / temperature homeostasis / response to pain / cellular response to alkaloid / calcium ion import across plasma membrane / diet induced thermogenesis / behavioral response to pain / 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 / extracellular ligand-gated monoatomic ion channel activity / monoatomic cation channel activity / monoatomic ion transmembrane transport / sensory perception of pain / : / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / phosphoprotein binding / calcium ion transmembrane transport / 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 / positive regulation of cytosolic calcium ion concentration / cellular response to heat / 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 / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
![]() | Arnold WR / Julius D / 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 | ![]() | 16.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.7 KB 15.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.7 KB | Display | ![]() |
Images | ![]() | 75.2 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 218.9 MB 218.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8u3aMC ![]() 8t0cC ![]() 8t0eC ![]() 8t0yC ![]() 8t10C ![]() 8t3lC ![]() 8t3mC ![]() 8u2zC ![]() 8u30C ![]() 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 monomer bound with PI-Br4 in Conformation 1 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.644 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: TRPV1 monomer bound with PI-Br4 in Conformation 1 half map 2
File | emd_41855_half_map_1.map | ||||||||||||
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Annotation | TRPV1 monomer bound with PI-Br4 in Conformation 1 half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: TRPV1 monomer bound with PI-Br4 in Conformation 1 half map 1
File | emd_41855_half_map_2.map | ||||||||||||
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Annotation | TRPV1 monomer bound with PI-Br4 in Conformation 1 half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : TRPV1 in nanodisc bound with PI-Br4 in Conformation 1 (monomer)
Entire | Name: TRPV1 in nanodisc bound with PI-Br4 in Conformation 1 (monomer) |
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Components |
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-Supramolecule #1: TRPV1 in nanodisc bound with PI-Br4 in Conformation 1 (monomer)
Supramolecule | Name: TRPV1 in nanodisc bound with PI-Br4 in Conformation 1 (monomer) 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: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 72.888227 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MGSRLYDRRS IFDAVAQSNC QELESLLPFL QRSKKRLTDS EFKDPETGKT CLLKAMLNLH NGQNDTIALL LDVARKTDSL KQFVNASYT DSYYKGQTAL HIAIERRNMT LVTLLVENGA DVQAAANGDF FKKTKGRPGF YFGELPLSLA ACTNQLAIVK F LLQNSWQP ...String: MGSRLYDRRS IFDAVAQSNC QELESLLPFL QRSKKRLTDS EFKDPETGKT CLLKAMLNLH NGQNDTIALL LDVARKTDSL KQFVNASYT DSYYKGQTAL HIAIERRNMT LVTLLVENGA DVQAAANGDF FKKTKGRPGF YFGELPLSLA ACTNQLAIVK F LLQNSWQP ADISARDSVG NTVLHALVEV ADNTVDNTKF VTSMYNEILI LGAKLHPTLK LEEITNRKGL TPLALAASSG KI GVLAYIL QREIHEPECR HLSRKFTEWA YGPVHSSLYD LSCIDTCEKN SVLEVIAYSS SETPNRHDML LVEPLNRLLQ DKW DRFVKR IFYFNFFVYC LYMIIFTAAA YYRPVEGLPP YKLKNTVGDY FRVTGEILSV SGGVYFFFRG IQYFLQRRPS LKSL FVDSY SEILFFVQSL FMLVSVVLYF SQRKEYVASM VFSLAMGWTN MLYYTRGFQQ MGIYAVMIEK MILRDLCRFM FVYLV FLFG FSTAVVTLIE DGKYNSLYST CLELFKFTIG MGDLEFTENY DFKAVFIILL LAYVILTYIL LLNMLIALMG ETVNKI AQE SKNIWKLQRA ITILDTEKSF LKCMRKAFRS GKLLQVGFTP DGKDDYRWCF RVDEVNWTTW NTNVGIINED PG UniProtKB: Transient receptor potential cation channel subfamily V member 1 |
-Macromolecule #2: (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R...
Macromolecule | Name: (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9R,10S)-9,10-dibromooctadecanoate type: ligand / ID: 2 / Number of copies: 1 / Formula: VPN |
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Molecular weight | Theoretical: 1.182722 KDa |
-Macromolecule #3: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PCW |
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Molecular weight | Theoretical: 787.121 Da |
Chemical component information | ![]() ChemComp-PCW: |
-Macromolecule #4: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 4 / Number of copies: 1 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 12 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-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 BIOQUANTUM (6k x 4k) / Average electron dose: 47.2 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 |