5l4e - Revision history

OCA at 16:06, 4 October 2023

OCA — Wed, 04 Oct 2023 16:06:30 GMT

←Older revision		Revision as of 16:06, 4 October 2023
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	<StructureSection load='5l4e' size='340' side='right'caption='[[5l4e]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='5l4e' size='340' side='right'caption='[[5l4e]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l4e]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Gloeobacter Gloeobacter]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L4E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5L4E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l4e]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Gloeobacter Gloeobacter]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5L4E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=EDP:5-ETHYL-5-[(2R)-PENTAN-2-YL]-2-THIOXODIHYDROPYRIMIDINE-4,6(1H,5H)-DIONE'>EDP</scene>~~</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.5Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glvI, glr4197 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33071 Gloeobacter])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=EDP:5-ETHYL-5-[(2R)-PENTAN-2-YL]-2-THIOXODIHYDROPYRIMIDINE-4,6(1H,5H)-DIONE'>EDP</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5l4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l4e OCA], [~~http~~://pdbe.org/5l4e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5l4e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5l4e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5l4e ProSAT]</span></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=5l4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l4e OCA], [https://pdbe.org/5l4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5l4e RCSB], [https://www.ebi.ac.uk/pdbsum/5l4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5l4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GLIC_GLOVI GLIC_GLOVI]] Cationic channel with similar permeabilities for Na(+) and K(+), that is activated by an increase of the proton concentration on the extracellular side. Displays no permeability for chloride ions. Shows slow kinetics of activation, no desensitization and a single channel conductance of 8 pS. Might contribute to adaptation to external pH change.<ref>PMID:17167423</ref>	+	[https://www.uniprot.org/uniprot/GLIC_GLOVI GLIC_GLOVI] Cationic channel with similar permeabilities for Na(+) and K(+), that is activated by an increase of the proton concentration on the extracellular side. Displays no permeability for chloride ions. Shows slow kinetics of activation, no desensitization and a single channel conductance of 8 pS. Might contribute to adaptation to external pH change.<ref>PMID:17167423</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Gloeobacter]]		[[Category: Gloeobacter]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Delarue, M]]	+	[[Category: Delarue M]]
-	[[Category: Fourati, Z]]	+	[[Category: Fourati Z]]
-	[[Category: Ruza~~, R R]]~~	+	[[Category: Ruza RR]]
-	~~[[Category: Barbiturate]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 06:43, 5 August 2020

OCA — Wed, 05 Aug 2020 06:43:28 GMT

←Older revision		Revision as of 06:43, 5 August 2020
Line 1:		Line 1:

	==X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with thiopental==		==X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with thiopental==
-	<StructureSection load='5l4e' size='340' side='right' caption='[[5l4e]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='5l4e' size='340' side='right'caption='[[5l4e]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l4e]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L4E OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5L4E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l4e]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Gloeobacter Gloeobacter]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L4E OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5L4E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=EDP:5-ETHYL-5-[(2R)-PENTAN-2-YL]-2-THIOXODIHYDROPYRIMIDINE-4,6(1H,5H)-DIONE'>EDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=EDP:5-ETHYL-5-[(2R)-PENTAN-2-YL]-2-THIOXODIHYDROPYRIMIDINE-4,6(1H,5H)-DIONE'>EDP</scene></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=5l4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l4e OCA], [http://pdbe.org/5l4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l4e RCSB], [http://www.ebi.ac.uk/pdbsum/5l4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l4e ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glvI, glr4197 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33071 Gloeobacter])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5l4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l4e OCA], [http://pdbe.org/5l4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l4e RCSB], [http://www.ebi.ac.uk/pdbsum/5l4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5l4e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5l4e" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ion channels 3D structures\|Ion channels 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Gloeobacter]]
		+	[[Category: Large Structures]]
	[[Category: Delarue, M]]		[[Category: Delarue, M]]
	[[Category: Fourati, Z]]		[[Category: Fourati, Z]]

OCA at 09:20, 2 January 2017

OCA — Mon, 02 Jan 2017 09:20:14 GMT

←Older revision		Revision as of 09:20, 2 January 2017
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GLIC_GLOVI GLIC_GLOVI]] Cationic channel with similar permeabilities for Na(+) and K(+), that is activated by an increase of the proton concentration on the extracellular side. Displays no permeability for chloride ions. Shows slow kinetics of activation, no desensitization and a single channel conductance of 8 pS. Might contribute to adaptation to external pH change.<ref>PMID:17167423</ref>		[[http://www.uniprot.org/uniprot/GLIC_GLOVI GLIC_GLOVI]] Cationic channel with similar permeabilities for Na(+) and K(+), that is activated by an increase of the proton concentration on the extracellular side. Displays no permeability for chloride ions. Shows slow kinetics of activation, no desensitization and a single channel conductance of 8 pS. Might contribute to adaptation to external pH change.<ref>PMID:17167423</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Barbiturates induce anesthesia by modulating the activity of anionic and cationic pentameric ligand-gated ion channels (pLGICs). Despite more than a century of use in clinical practice, the prototypic binding site for this class of drugs within pLGICs is yet to be described. In this study, we present the first X-ray structures of barbiturates bound to GLIC, a cationic prokaryotic pLGIC with excellent structural homology to other relevant channels sensitive to general anesthetics and, as shown here, to barbiturates, at clinically-relevant concentrations. Several derivatives of barbiturates containing anomalous scatterers were synthesized and helped to unambiguously identify a unique barbiturate binding site within the central ion channel pore in a closed conformation. In addition, docking calculations around the observed binding site for all three states of the receptor, including a model of the desensitized state, showed that barbiturates preferentially stabilize the closed state. The identification of this pore binding site sheds light on the mechanism of barbiturates inhibition of cationic pLGICs and allows the rationalisation of several structural and functional features previously observed for barbiturates.
		+
		+	Barbiturates bind in the GLIC ion channel pore and cause inhibition by stabilizing a closed state.,Fourati Z, Ruza RR, Laverty D, Drege E, Delarue-Cochin S, Joseph D, Koehl P, Smart T, Delarue M J Biol Chem. 2016 Dec 16. pii: jbc.M116.766964. PMID:27986812<ref>PMID:27986812</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5l4e" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:43, 22 December 2016

OCA — Thu, 22 Dec 2016 21:43:20 GMT

←Older revision		Revision as of 21:43, 22 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5l4e is ON HOLD until Paper Publication~~	+	==X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with thiopental==
-		+	<StructureSection load='5l4e' size='340' side='right' caption='[[5l4e]], [[Resolution\|resolution]] 3.50Å' scene=''>
-	~~Authors: Fourati, Z., Ruza, R.R., Delarue, M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5l4e]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5L4E FirstGlance]. <br>
-	~~Description:~~ X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with thiopental	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=EDP:5-ETHYL-5-[(2R)-PENTAN-2-YL]-2-THIOXODIHYDROPYRIMIDINE-4,6(1H,5H)-DIONE'>EDP</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5l4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l4e OCA], [http://pdbe.org/5l4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l4e RCSB], [http://www.ebi.ac.uk/pdbsum/5l4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l4e ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GLIC_GLOVI GLIC_GLOVI]] Cationic channel with similar permeabilities for Na(+) and K(+), that is activated by an increase of the proton concentration on the extracellular side. Displays no permeability for chloride ions. Shows slow kinetics of activation, no desensitization and a single channel conductance of 8 pS. Might contribute to adaptation to external pH change.<ref>PMID:17167423</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Delarue, M]]
	[[Category: Fourati, Z]]		[[Category: Fourati, Z]]
-	[[Category: Ruza, R.R]]	+	[[Category: Ruza, R R]]
-	[[Category: ~~Delarue, M~~]]	+	[[Category: Barbiturate]]
		+	[[Category: Membrane protein]]
		+	[[Category: Transport protein]]

OCA at 13:52, 20 June 2016

OCA — Mon, 20 Jun 2016 13:52:34 GMT

←Older revision		Revision as of 13:52, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5l4e is ON HOLD	+	The entry 5l4e is ON HOLD until Paper Publication

-	Authors: Fourati, Z., ~~Reynholds~~ Ruza, R., Delarue, M.	+	Authors: Fourati, Z., Ruza, R.R., Delarue, M.

	Description: X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with thiopental		Description: X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with thiopental
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Reynholds Ruza, R]]
	[[Category: Fourati, Z]]		[[Category: Fourati, Z]]
		+	[[Category: Ruza, R.R]]
	[[Category: Delarue, M]]		[[Category: Delarue, M]]

OCA: Protected "5l4e" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:29:28 GMT

Protected "5l4e" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:29, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5l4e is ON HOLD Authors: Fourati, Z., Reynholds Ruza, R., Delarue, M. Description: X-ray structure of the 2-22' locally-closed mutant of GLIC in co...

OCA — Wed, 01 Jun 2016 14:29:27 GMT

New page: '''Unreleased structure''' The entry 5l4e is ON HOLD Authors: Fourati, Z., Reynholds Ruza, R., Delarue, M. Description: X-ray structure of the 2-22' locally-closed mutant of GLIC in co...

New page

'''Unreleased structure'''

The entry 5l4e is ON HOLD

Authors: Fourati, Z., Reynholds Ruza, R., Delarue, M.

Description: X-ray structure of the 2-22' locally-closed mutant of GLIC in complex with thiopental
[[Category: Unreleased Structures]]
[[Category: Reynholds Ruza, R]]
[[Category: Fourati, Z]]
[[Category: Delarue, M]]