4dw1 - Revision history

OCA at 08:40, 21 September 2022

OCA — Wed, 21 Sep 2022 08:40:50 GMT

←Older revision		Revision as of 08:40, 21 September 2022
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	==Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms==		==Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms==
-	<StructureSection load='4dw1' size='340' side='right' caption='[[4dw1]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='4dw1' size='340' side='right'caption='[[4dw1]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dw1]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DW1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dw1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DW1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA~~-D-~~MANNOSE~~'>~~MAN~~</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dw0\|4dw0]]</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=4dw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dw1 OCA], [https://pdbe.org/4dw1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dw1 RCSB], [https://www.ebi.ac.uk/pdbsum/4dw1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dw1 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2rx4a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])~~</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=4dw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dw1 OCA], [~~http~~://pdbe.org/4dw1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dw1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dw1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dw1 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/F8W463_DANRE F8W463_DANRE]] Receptor for ATP that acts as a ligand-gated ion channel.[PIRNR:PIRNR005713][RuleBase:RU000681]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Ion channels\|Ion channels]]	+	*[[Ion channels 3D structures\|Ion channels 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
-	[[Category: ~~Gouaux, E~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Hattori, M~~]]	+	[[Category: Gouaux E]]
-	[[Category: ~~Ion channel]]~~	+	[[Category: Hattori M]]
-	~~[[Category: Transport protein~~]]	+

OCA at 02:43, 11 December 2016

OCA — Sun, 11 Dec 2016 02:43:44 GMT

←Older revision		Revision as of 02:43, 11 December 2016
Line 1:		Line 1:
		+
	==Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms==		==Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms==
	<StructureSection load='4dw1' size='340' side='right' caption='[[4dw1]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='4dw1' size='340' side='right' caption='[[4dw1]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dw1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Danio_rerio Danio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dw1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DW1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dw0\|4dw0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dw0\|4dw0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2rx4a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 ~~Danio~~ rerio])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2rx4a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</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=4dw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dw1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dw1 RCSB], [http://www.ebi.ac.uk/pdbsum/4dw1 PDBsum]</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=4dw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dw1 OCA], [http://pdbe.org/4dw1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dw1 RCSB], [http://www.ebi.ac.uk/pdbsum/4dw1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dw1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4dw1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ion channels\|Ion channels]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Danio~~ rerio]]	+	[[Category: Brachidanio rerio]]
	[[Category: Gouaux, E]]		[[Category: Gouaux, E]]
	[[Category: Hattori, M]]		[[Category: Hattori, M]]
	[[Category: Ion channel]]		[[Category: Ion channel]]
	[[Category: Transport protein]]		[[Category: Transport protein]]

OCA at 15:49, 9 December 2014

OCA — Tue, 09 Dec 2014 15:49:19 GMT

←Older revision		Revision as of 15:49, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4dw1.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms==
		+	<StructureSection load='4dw1' size='340' side='right' caption='[[4dw1]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4dw1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DW1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dw0\|4dw0]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p2rx4a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Danio rerio])</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=4dw1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dw1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dw1 RCSB], [http://www.ebi.ac.uk/pdbsum/4dw1 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	P2X receptors are trimeric ATP-activated ion channels permeable to Na+, K+ and Ca2+. The seven P2X receptor subtypes are implicated in physiological processes that include modulation of synaptic transmission, contraction of smooth muscle, secretion of chemical transmitters and regulation of immune responses. Despite the importance of P2X receptors in cellular physiology, the three-dimensional composition of the ATP-binding site, the structural mechanism of ATP-dependent ion channel gating and the architecture of the open ion channel pore are unknown. Here we report the crystal structure of the zebrafish P2X4 receptor in complex with ATP and a new structure of the apo receptor. The agonist-bound structure reveals a previously unseen ATP-binding motif and an open ion channel pore. ATP binding induces cleft closure of the nucleotide-binding pocket, flexing of the lower body beta-sheet and a radial expansion of the extracellular vestibule. The structural widening of the extracellular vestibule is directly coupled to the opening of the ion channel pore by way of an iris-like expansion of the transmembrane helices. The structural delineation of the ATP-binding site and the ion channel pore, together with the conformational changes associated with ion channel gating, will stimulate development of new pharmacological agents.

-	~~{{STRUCTURE_4dw1\| PDB=4dw1 \| SCENE= }}~~	+	Molecular mechanism of ATP binding and ion channel activation in P2X receptors.,Hattori M, Gouaux E Nature. 2012 May 10;485(7397):207-12. PMID:22535247<ref>PMID:22535247</ref>

-	~~===Crystal structure~~ of the ~~ATP-gated P2X4 ion channel in the ATP-bound, open state at 2~~.~~8 Angstroms===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22535247}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[4dw1]] is a 1 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DW1 OCA].~~	+	</StructureSection>
	[[Category: Danio rerio]]		[[Category: Danio rerio]]
-	[[Category: Gouaux, E.]]	+	[[Category: Gouaux, E]]
-	[[Category: Hattori, M.]]	+	[[Category: Hattori, M]]
	[[Category: Ion channel]]		[[Category: Ion channel]]
	[[Category: Transport protein]]		[[Category: Transport protein]]

OCA at 08:16, 9 January 2013

OCA — Wed, 09 Jan 2013 08:16:41 GMT

←Older revision		Revision as of 08:16, 9 January 2013
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-	[[Image:4dw1.~~jpg~~\|left\|200px]]	+	[[Image:4dw1.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_4dw1", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_4dw1\| PDB=4dw1 \| SCENE= }}		{{STRUCTURE_4dw1\| PDB=4dw1 \| SCENE= }}

	===Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms===		===Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms===

		+	{{ABSTRACT_PUBMED_22535247}}

	==About this Structure==		==About this Structure==

OCA at 09:27, 25 April 2012

OCA — Wed, 25 Apr 2012 09:27:45 GMT

←Older revision		Revision as of 09:27, 25 April 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:4dw1.jpg\|left\|200px]]

-	The ~~entry 4dw1~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_4dw1", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_4dw1\| PDB=4dw1 \| SCENE= }}

-	~~Authors: Hattori~~, ~~M., Gouaux, E~~.	+	===Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms===

-	~~Description: Crystal~~ structure ~~of the ATP~~-~~gated P2X4 ion channel in the ATP-bound~~, ~~open state at 2~~.~~8 Angstroms~~	+
		+	==About this Structure==
		+	[[4dw1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DW1 OCA].
		+	[[Category: Danio rerio]]
		+	[[Category: Gouaux, E.]]
		+	[[Category: Hattori, M.]]
		+	[[Category: Ion channel]]
		+	[[Category: Transport protein]]

OCA at 05:27, 8 March 2012

OCA — Thu, 08 Mar 2012 05:27:11 GMT

←Older revision		Revision as of 05:27, 8 March 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4dw1 is ON HOLD	+	The entry 4dw1 is ON HOLD until Paper Publication

	Authors: Hattori, M., Gouaux, E.		Authors: Hattori, M., Gouaux, E.

	Description: Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms		Description: Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms

OCA: Protected "4dw1" [edit=sysop:move=sysop]

OCA — Wed, 29 Feb 2012 08:30:26 GMT

Protected "4dw1" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:30, 29 February 2012

OCA: New page: '''Unreleased structure''' The entry 4dw1 is ON HOLD Authors: Hattori, M., Gouaux, E. Description: Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2...

OCA — Wed, 29 Feb 2012 08:30:25 GMT

New page: '''Unreleased structure''' The entry 4dw1 is ON HOLD Authors: Hattori, M., Gouaux, E. Description: Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2...

New page

'''Unreleased structure'''

The entry 4dw1 is ON HOLD

Authors: Hattori, M., Gouaux, E.

Description: Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms