6pkx - Revision history

OCA at 04:30, 11 April 2020

OCA — Sat, 11 Apr 2020 04:30:03 GMT

←Older revision		Revision as of 04:30, 11 April 2020
Line 3:		Line 3:
	<SX load='6pkx' size='340' side='right' viewer='molstar' caption='[[6pkx]], [[Resolution\|resolution]] 4.20Å' scene=''>		<SX load='6pkx' size='340' side='right' viewer='molstar' caption='[[6pkx]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pkx]] is a 4 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=6PKX OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PKX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pkx]] is a 4 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=6PKX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PKX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpm2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpm2 ([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=6pkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkx OCA], [http://pdbe.org/6pkx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pkx RCSB], [http://www.ebi.ac.uk/pdbsum/6pkx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkx 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=6pkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkx OCA], [http://pdbe.org/6pkx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pkx RCSB], [http://www.ebi.ac.uk/pdbsum/6pkx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:24, 6 March 2020

OCA — Fri, 06 Mar 2020 23:24:40 GMT

←Older revision		Revision as of 23:24, 6 March 2020
Line 1:		Line 1:

	==Cryo-EM structure of the zebrafish TRPM2 channel in the presence of ADPR and Ca2+==		==Cryo-EM structure of the zebrafish TRPM2 channel in the presence of ADPR and Ca2+==
-	<~~StructureSection~~ load='6pkx' size='340' side='right'caption='[[6pkx]], [[Resolution\|resolution]] 4.20Å' scene=''>	+	<SX load='6pkx' size='340' side='right' viewer='molstar' caption='[[6pkx]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6pkx]] is a 4 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=6PKX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PKX FirstGlance]. <br>		<table><tr><td colspan='2'>[[6pkx]] is a 4 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=6PKX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PKX FirstGlance]. <br>
Line 21:		Line 21:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Brachidanio rerio]]		[[Category: Brachidanio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 09:18, 27 November 2019

OCA — Wed, 27 Nov 2019 09:18:33 GMT

←Older revision		Revision as of 09:18, 27 November 2019
Line 3:		Line 3:
	<StructureSection load='6pkx' size='340' side='right'caption='[[6pkx]], [[Resolution\|resolution]] 4.20Å' scene=''>		<StructureSection load='6pkx' size='340' side='right'caption='[[6pkx]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pkx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PKX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PKX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pkx]] is a 4 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=6PKX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PKX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trpm2 ([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=6pkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkx OCA], [http://pdbe.org/6pkx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pkx RCSB], [http://www.ebi.ac.uk/pdbsum/6pkx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkx 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=6pkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkx OCA], [http://pdbe.org/6pkx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pkx RCSB], [http://www.ebi.ac.uk/pdbsum/6pkx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkx ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The transient receptor potential melastatin 2 (TRPM2) channel plays a key role in redox sensation in many cell types. Channel activation requires binding of both ADP-ribose (ADPR) and Ca(2+). The recently published TRPM2 structures from Danio rerio in the ligand-free and the ADPR/Ca(2+)-bound conditions represent the channel in closed and open states, which uncovered substantial tertiary and quaternary conformational rearrangements. However, it is unclear how these rearrangements are achieved within the tetrameric channel during channel gating. Here we report the cryo-electron microscopy structures of Danio rerio TRPM2 in the absence of ligands, in complex with Ca(2+) alone, and with both ADPR and Ca(2+), resolved to ~4.3 A, ~3.8 A, and ~4.2 A, respectively. In contrast to the published results, our studies capture ligand-bound TRPM2 structures in two-fold symmetric intermediate states, offering a glimpse of the structural transitions that bridge the closed and open conformations.
		+
		+	Visualizing structural transitions of ligand-dependent gating of the TRPM2 channel.,Yin Y, Wu M, Hsu AL, Borschel WF, Borgnia MJ, Lander GC, Lee SY Nat Commun. 2019 Aug 20;10(1):3740. doi: 10.1038/s41467-019-11733-5. PMID:31431622<ref>PMID:31431622</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6pkx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Borgnia, M J]]		[[Category: Borgnia, M J]]

OCA at 15:33, 28 August 2019

OCA — Wed, 28 Aug 2019 15:33:58 GMT

←Older revision		Revision as of 15:33, 28 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6pkx ~~is ON HOLD~~	+	==Cryo-EM structure of the zebrafish TRPM2 channel in the presence of ADPR and Ca2+==
-		+	<StructureSection load='6pkx' size='340' side='right'caption='[[6pkx]], [[Resolution\|resolution]] 4.20Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6pkx]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PKX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PKX FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</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=6pkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pkx OCA], [http://pdbe.org/6pkx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pkx RCSB], [http://www.ebi.ac.uk/pdbsum/6pkx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pkx ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Borgnia, M J]]
		+	[[Category: Borschel, W F]]
		+	[[Category: Hsu, A L]]
		+	[[Category: Lander, G C]]
		+	[[Category: Lee, S Y]]
		+	[[Category: Wu, M]]
		+	[[Category: Yin, Y]]
		+	[[Category: Adp-ribose]]
		+	[[Category: Calcium-permeable ion channel]]
		+	[[Category: Ion channel]]
		+	[[Category: Redox sensor]]
		+	[[Category: Transport protein]]
		+	[[Category: Trp channel]]
		+	[[Category: Trpm channel]]
		+	[[Category: Warmth sensor]]

OCA: Protected "6pkx" [edit=sysop:move=sysop]

OCA — Wed, 10 Jul 2019 04:12:11 GMT

Protected "6pkx" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:12, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pkx is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 Jul 2019 04:12:09 GMT

New page: '''Unreleased structure''' The entry 6pkx is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6pkx is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]