Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of TRPV1 modulation by endogenous bioactive lipids.
Journal, issue, pages	Nat Struct Mol Biol, Year 2024
Publish date	May 2, 2024
Authors	William R Arnold / Adamo Mancino / Frank R Moss / Adam Frost / David Julius / Yifan Cheng /
PubMed 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.
External links	Nat Struct Mol Biol / PubMed:38698206
Methods	EM (single particle)
Resolution	2.2 - 3.7 Å
Structure data	40940 8t0c EMDB-40940, PDB-8t0c: TRPV1 in Nanodisc bound with lysophosphatidic acid in all four monomers Method: EM (single particle) / Resolution: 3.5 Å 40941 8t0e EMDB-40941, PDB-8t0e: TRPV1 in Nanodisc not bound with lysophosphatidic acid (apo) Method: EM (single particle) / Resolution: 3.3 Å 40949 8t0y EMDB-40949, PDB-8t0y: TRPV1 in nanodisc bound with one LPA in one monomer Method: EM (single particle) / Resolution: 3.5 Å 40951 8t10 EMDB-40951, PDB-8t10: TRPV1 in nanodisc bound with two LPA molecules in opposite monomers Method: EM (single particle) / Resolution: 3.7 Å 41005 8t3l EMDB-41005, PDB-8t3l: TRPV1 in nanodisc bound with 2 LPA molecules in neighboring monomers Method: EM (single particle) / Resolution: 3.6 Å 41006 8t3m EMDB-41006, PDB-8t3m: TRPV1 in nanodisc bound with 3 LPA molecules Method: EM (single particle) / Resolution: 3.5 Å 41847 8u2z EMDB-41847, PDB-8u2z: TRPV1 in nanodisc bound with diC8-PIP2 in the dilated state Method: EM (single particle) / Resolution: 3.6 Å 41848 8u30 EMDB-41848, PDB-8u30: TRPV1 in nanodisc bound with diC8-PIP2 in the closed state Method: EM (single particle) / Resolution: 3.0 Å 41855 8u3a EMDB-41855, PDB-8u3a: TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer) Method: EM (single particle) / Resolution: 2.3 Å 41857 8u3c EMDB-41857, PDB-8u3c: TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 2 (monomer) Method: EM (single particle) / Resolution: 2.3 Å 41864 8u3j EMDB-41864, PDB-8u3j: TRPV1 in nanodisc bound with empty vanilloid binding pocket at 4C Method: EM (single particle) / Resolution: 2.9 Å 41866 8u3l EMDB-41866, PDB-8u3l: TRPV1 in nanodisc bound with empty vanilloid binding pocket at 25C Method: EM (single particle) / Resolution: 3.7 Å 41873 8u43 EMDB-41873, PDB-8u43: TRPV1 in nanodisc bound with PIP2-Br4 Method: EM (single particle) / Resolution: 2.4 Å 41879 8u4d EMDB-41879, PDB-8u4d: TRPV1 in nanodisc bound with PI-Br4, consensus structure Method: EM (single particle) / Resolution: 2.2 Å
Chemicals	ChemComp-NKN: (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate ChemComp-NA: Unknown entry ChemComp-8IJ: (2R)-3-{[(R)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate ChemComp-HOH: WATER / Water ChemComp-85R: [(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{S},3~{S},5~{R},6~{S})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate ChemComp-PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate ChemComp-PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipidYM ChemComp-CLR: CHOLESTEROL / Cholesterol ChemComp, No image ChemComp-VPN: Unknown entry ChemComp-3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Phosphatidic acid ChemComp, No image ChemComp-V5H*: Unknown entry
Source	rattus norvegicus (Norway rat)
Keywords	MEMBRANE PROTEIN / TRPV1 / lysophosphatidic acid / TRPV1 in nanodisc bound with one LPA in one monomer / TRPV1 in nanodisc bound with two LPA molecules in opposite monomers / TRPV1 in nanodisc bound with diC8-PIP2 in the dilated state / TRPV1 in nanodisc bound with diC8-PIP2 in the closed state / TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer) / TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 2 (monomer) / TRPV1 in nanodisc bound with empty vanilloid binding pocket at 4C / TRPV1 in nanodisc bound with empty vanilloid binding pocket at 25C / TRPV1 in nanodisc bound with PIP2-Br4 MEMBRANE PROTEIN / TRPV1 in nanodisc bound with PI-Br4 / consensus structure MEMBRANE PROTEIN