5is0: Difference between revisions

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 ==Structure of TRPV1 in complex with capsazepine, determined in lipid nanodisc==
-<StructureSection load='5is0' size='340' side='right'caption='[[5is0]], [[Resolution|resolution]] 3.43&Aring;' scene=''>
+<SX load='5is0' size='340' side='right' viewer='molstar' caption='[[5is0]], [[Resolution|resolution]] 3.43&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5is0]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IS0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IS0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5is0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IS0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IS0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6ET:CAPSAZEPINE'>6ET</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.43&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5irx|5irx]], [[5irz|5irz]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6ET:CAPSAZEPINE'>6ET</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Trpv1, Vr1, Vr1l ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5is0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5is0 OCA], [https://pdbe.org/5is0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5is0 RCSB], [https://www.ebi.ac.uk/pdbsum/5is0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5is0 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5is0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5is0 OCA], [http://pdbe.org/5is0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5is0 RCSB], [http://www.ebi.ac.uk/pdbsum/5is0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5is0 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TRPV1_RAT TRPV1_RAT]] Receptor-activated non-selective calcium permeant cation channel involved in detection of noxious chemical and thermal stimuli. Seems to mediate proton influx and may be involved in intracellular acidosis in nociceptive neurons. May be involved in mediation of inflammatory pain and hyperalgesia. Sensitized by a phosphatidylinositol second messenger system activated by receptor tyrosine kinases, which involves PKC isozymes and PCL. Activation by vanilloids, like capsaicin, and temperatures higher than 42 degrees Celsius, exhibits a time- and Ca(2+)-dependent outward rectification, followed by a long-lasting refractory state. Mild extracellular acidic pH (6.5) potentiates channel activation by noxious heat and vanilloids, whereas acidic conditions (pH <6) directly activate the channel. Can be activated by endogenous compounds, including 12-hydroperoxytetraenoic acid and bradykinin. Acts as ionotropic endocannabinoid receptor with central neuromodulatory effects. Triggers a form of long-term depression (TRPV1-LTD) mediated by the endocannabinoid anandamine in the hippocampus and nucleus accumbens by affecting AMPA receptors endocytosis.<ref>PMID:9349813</ref> <ref>PMID:10644739</ref> <ref>PMID:11140687</ref> <ref>PMID:11418861</ref> <ref>PMID:12095983</ref> <ref>PMID:12194871</ref> <ref>PMID:12808128</ref> <ref>PMID:14523239</ref> <ref>PMID:12764195</ref> <ref>PMID:14630912</ref> <ref>PMID:15173182</ref> <ref>PMID:21076423</ref>
+[https://www.uniprot.org/uniprot/TRPV1_RAT TRPV1_RAT] Receptor-activated non-selective calcium permeant cation channel involved in detection of noxious chemical and thermal stimuli. Seems to mediate proton influx and may be involved in intracellular acidosis in nociceptive neurons. May be involved in mediation of inflammatory pain and hyperalgesia. Sensitized by a phosphatidylinositol second messenger system activated by receptor tyrosine kinases, which involves PKC isozymes and PCL. Activation by vanilloids, like capsaicin, and temperatures higher than 42 degrees Celsius, exhibits a time- and Ca(2+)-dependent outward rectification, followed by a long-lasting refractory state. Mild extracellular acidic pH (6.5) potentiates channel activation by noxious heat and vanilloids, whereas acidic conditions (pH <6) directly activate the channel. Can be activated by endogenous compounds, including 12-hydroperoxytetraenoic acid and bradykinin. Acts as ionotropic endocannabinoid receptor with central neuromodulatory effects. Triggers a form of long-term depression (TRPV1-LTD) mediated by the endocannabinoid anandamine in the hippocampus and nucleus accumbens by affecting AMPA receptors endocytosis.<ref>PMID:9349813</ref> <ref>PMID:10644739</ref> <ref>PMID:11140687</ref> <ref>PMID:11418861</ref> <ref>PMID:12095983</ref> <ref>PMID:12194871</ref> <ref>PMID:12808128</ref> <ref>PMID:14523239</ref> <ref>PMID:12764195</ref> <ref>PMID:14630912</ref> <ref>PMID:15173182</ref> <ref>PMID:21076423</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-When integral membrane proteins are visualized in detergents or other artificial systems, an important layer of information is lost regarding lipid interactions and their effects on protein structure. This is especially relevant to proteins for which lipids have both structural and regulatory roles. Here we demonstrate the power of combining electron cryo-microscopy with lipid nanodisc technology to ascertain the structure of the rat TRPV1 ion channel in a native bilayer environment. Using this approach, we determined the locations of annular and regulatory lipids and showed that specific phospholipid interactions enhance binding of a spider toxin to TRPV1 through formation of a tripartite complex. Furthermore, phosphatidylinositol lipids occupy the binding site for capsaicin and other vanilloid ligands, suggesting a mechanism whereby chemical or thermal stimuli elicit channel activation by promoting the release of bioactive lipids from a critical allosteric regulatory site.
-TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action.,Gao Y, Cao E, Julius D, Cheng Y Nature. 2016 May 18;534(7607):347-51. doi: 10.1038/nature17964. PMID:27281200<ref>PMID:27281200</ref>
+==See Also==
+*[[Ion channels 3D structures|Ion channels 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5is0" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Buffalo rat]]
 [[Category: Large Structures]]
-[[Category: Cao, E]]
+[[Category: Rattus norvegicus]]
-[[Category: Cheng, Y]]
+[[Category: Cao E]]
-[[Category: Gao, Y]]
+[[Category: Cheng Y]]
-[[Category: Julius, D]]
+[[Category: Gao Y]]
-[[Category: Interaction]]
+[[Category: Julius D]]
-[[Category: Ion channel]]
-[[Category: Lipid]]
-[[Category: Nanodisc]]
-[[Category: Transport protein]]
-[[Category: Trp]]
-[[Category: Vanilloid]]