5svm - Revision history

OCA at 15:33, 6 March 2024

2024-03-06T15:33:43Z

←Older revision		Revision as of 15:33, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5svm' size='340' side='right'caption='[[5svm]], [[Resolution\|resolution]] 3.09Å' scene=''>		<StructureSection load='5svm' size='340' side='right'caption='[[5svm]], [[Resolution\|resolution]] 3.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5svm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SVM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5SVM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5svm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SVM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6AT:2-(METHYLSULFANYL)ADENOSINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)'>6AT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 3.093Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5svj\|5svj]], [[5svk\|5svk]], [[5svl\|5svl]], [[5svp\|5svp]], [[5svq\|5svq]], [[5svr\|5svr]], [[5svs\|5svs]], [[5svt\|5svt]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6AT:2-(METHYLSULFANYL)ADENOSINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)'>6AT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">P2RX3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=5svm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5svm OCA], [https://pdbe.org/5svm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5svm RCSB], [https://www.ebi.ac.uk/pdbsum/5svm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5svm ProSAT]</span></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=5svm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5svm OCA], [~~http~~://pdbe.org/5svm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5svm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5svm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5svm ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/P2RX3_HUMAN P2RX3_HUMAN]] Receptor for ATP that acts as a ligand-gated ion channel.	+	[https://www.uniprot.org/uniprot/P2RX3_HUMAN P2RX3_HUMAN] Receptor for ATP that acts as a ligand-gated ion channel.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	P2X receptors are trimeric, non-selective cation channels activated by ATP that have important roles in the cardiovascular, neuronal and immune systems. Despite their central function in human physiology and although they are potential targets of therapeutic agents, there are no structures of human P2X receptors. The mechanisms of receptor desensitization and ion permeation, principles of antagonism, and complete structures of the pore-forming transmembrane domains of these receptors remain unclear. Here we report X-ray crystal structures of the human P2X3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/closed-pore/desensitized and antagonist-bound/closed states. The open state structure harbours an intracellular motif we term the 'cytoplasmic cap', which stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress. The competitive antagonists TNP-ATP and A-317491 stabilize the apo/resting state and reveal the interactions responsible for competitive inhibition. These structures illuminate the conformational rearrangements that underlie P2X receptor gating and provide a foundation for the development of new pharmacological agents.	+

-	X-ray structures define human P2X3 receptor gating cycle and antagonist action.,Mansoor SE, Lu W, Oosterheert W, Shekhar M, Tajkhorshid E, Gouaux E Nature. 2016 Sep 14. doi: 10.1038/nature19367. PMID:27626375<ref>PMID:27626375</ref>	+	==See Also==
-		+	*[[Ion channels 3D structures\|Ion channels 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 5svm" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gouaux, E]]	+	[[Category: Gouaux E]]
-	[[Category: Lu, W]]	+	[[Category: Lu W]]
-	[[Category: Mansoor~~, S E~~]]	+	[[Category: Mansoor SE]]
-	[[Category: Oosterheert, W]]	+	[[Category: Oosterheert W]]
-	[[Category: Shekhar, M]]	+	[[Category: Shekhar M]]
-	[[Category: Tajkhorshid, E]]	+	[[Category: Tajkhorshid E]]
-	~~[[Category: Desensitized state]]~~	+
-	~~[[Category: Ion channel]]~~	+
-	~~[[Category: Membrane protein~~]]	+

OCA at 11:12, 16 September 2020

2020-09-16T11:12:23Z

←Older revision		Revision as of 11:12, 16 September 2020
Line 1:		Line 1:

	==Crystal structure of the ATP-gated human P2X3 ion channel bound to agonist 2-methylthio-ATP in the desensitized state==		==Crystal structure of the ATP-gated human P2X3 ion channel bound to agonist 2-methylthio-ATP in the desensitized state==
-	<StructureSection load='5svm' size='340' side='right' caption='[[5svm]], [[Resolution\|resolution]] 3.09Å' scene=''>	+	<StructureSection load='5svm' size='340' side='right'caption='[[5svm]], [[Resolution\|resolution]] 3.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5svm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SVM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5SVM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5svm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SVM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5SVM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6AT:2-(METHYLSULFANYL)ADENOSINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)'>6AT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6AT:2-(METHYLSULFANYL)ADENOSINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)'>6AT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5svj\|5svj]], [[5svk\|5svk]], [[5svl\|5svl]], [[5svp\|5svp]], [[5svq\|5svq]], [[5svr\|5svr]], [[5svs\|5svs]], [[5svt\|5svt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5svj\|5svj]], [[5svk\|5svk]], [[5svl\|5svl]], [[5svp\|5svp]], [[5svq\|5svq]], [[5svr\|5svr]], [[5svs\|5svs]], [[5svt\|5svt]]</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=5svm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5svm OCA], [http://pdbe.org/5svm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5svm RCSB], [http://www.ebi.ac.uk/pdbsum/5svm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5svm ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">P2RX3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5svm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5svm OCA], [http://pdbe.org/5svm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5svm RCSB], [http://www.ebi.ac.uk/pdbsum/5svm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5svm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Gouaux, E]]		[[Category: Gouaux, E]]
	[[Category: Lu, W]]		[[Category: Lu, W]]

OCA at 16:56, 3 October 2016

2016-10-03T16:56:09Z

←Older revision		Revision as of 16:56, 3 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5svm is ~~ON HOLD~~	+	==Crystal structure of the ATP-gated human P2X3 ion channel bound to agonist 2-methylthio-ATP in the desensitized state==
		+	<StructureSection load='5svm' size='340' side='right' caption='[[5svm]], [[Resolution\|resolution]] 3.09Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5svm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SVM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6AT:2-(METHYLSULFANYL)ADENOSINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)'>6AT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5svj\|5svj]], [[5svk\|5svk]], [[5svl\|5svl]], [[5svp\|5svp]], [[5svq\|5svq]], [[5svr\|5svr]], [[5svs\|5svs]], [[5svt\|5svt]]</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=5svm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5svm OCA], [http://pdbe.org/5svm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5svm RCSB], [http://www.ebi.ac.uk/pdbsum/5svm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5svm ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/P2RX3_HUMAN P2RX3_HUMAN]] Receptor for ATP that acts as a ligand-gated ion channel.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	P2X receptors are trimeric, non-selective cation channels activated by ATP that have important roles in the cardiovascular, neuronal and immune systems. Despite their central function in human physiology and although they are potential targets of therapeutic agents, there are no structures of human P2X receptors. The mechanisms of receptor desensitization and ion permeation, principles of antagonism, and complete structures of the pore-forming transmembrane domains of these receptors remain unclear. Here we report X-ray crystal structures of the human P2X3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/closed-pore/desensitized and antagonist-bound/closed states. The open state structure harbours an intracellular motif we term the 'cytoplasmic cap', which stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress. The competitive antagonists TNP-ATP and A-317491 stabilize the apo/resting state and reveal the interactions responsible for competitive inhibition. These structures illuminate the conformational rearrangements that underlie P2X receptor gating and provide a foundation for the development of new pharmacological agents.

-	~~Authors~~:	+	X-ray structures define human P2X3 receptor gating cycle and antagonist action.,Mansoor SE, Lu W, Oosterheert W, Shekhar M, Tajkhorshid E, Gouaux E Nature. 2016 Sep 14. doi: 10.1038/nature19367. PMID:27626375<ref>PMID:27626375</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5svm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gouaux, E]]
		+	[[Category: Lu, W]]
		+	[[Category: Mansoor, S E]]
		+	[[Category: Oosterheert, W]]
		+	[[Category: Shekhar, M]]
		+	[[Category: Tajkhorshid, E]]
		+	[[Category: Desensitized state]]
		+	[[Category: Ion channel]]
		+	[[Category: Membrane protein]]

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

2016-09-09T15:19:43Z

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

←Older revision

Revision as of 15:19, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5svm is ON HOLD Authors: Description: Category: Unreleased Structures

2016-09-09T15:19:42Z

New page: '''Unreleased structure''' The entry 5svm is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5svm is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]