5jdl - Revision history

OCA at 11:00, 6 September 2023

2023-09-06T11:00:23Z

← Older revision		Revision as of 11:00, 6 September 2023
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	<StructureSection load='5jdl' size='340' side='right'caption='[[5jdl]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5jdl' size='340' side='right'caption='[[5jdl]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jdl]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Metja Metja~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JDL FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jdl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JDL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MYS:PENTADECANE'>MYS</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 2.904Å</td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jdq\|5jdq]], [[5jdn\|5jdn]], [[5jdm\|5jdm]], [[5jdh\|5jdh]], [[5jdg\|5jdg]], [[5jdf\|5jdf]], [[5hwx\|5hwx]], [[5hwy\|5hwy]], [[5hxc\|5hxc]], [[5hxe\|5hxe]], [[5hxh\|5hxh]], [[5hxr\|5hxr]], [[5hxs\|5hxs]], [[5hya\|5hya]]</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MYS:PENTADECANE'>MYS</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ0091 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])~~</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=5jdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdl OCA], [https://pdbe.org/5jdl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jdl RCSB], [https://www.ebi.ac.uk/pdbsum/5jdl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jdl 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=5jdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdl OCA], [~~http~~://pdbe.org/5jdl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jdl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jdl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jdl ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Y091_METJA Y091_METJA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5jdl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jdl" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Sodium-calcium exchanger\|Sodium-calcium exchanger]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Metja~~]]		[[Category: Methanocaldococcus jannaschii DSM 2661]]
	[[Category: Faraldo-Gomez~~, J D~~]]		[[Category: Faraldo-Gomez JD]]
	[[Category: Jiang~~, Y X~~]]		[[Category: Jiang YX]]
	[[Category: Liao, J]]		[[Category: Liao J]]
	~~[[Category: Calcium signalling]]~~
	~~[[Category: Induced conformational change]]~~
	~~[[Category: Membrane protein]]~~
	~~[[Category: Membrane transporter]]~~
	~~[[Category: Na+/ca2+ exchange~~]]

OCA at 16:22, 20 November 2019

2019-11-20T16:22:07Z

← Older revision		Revision as of 16:22, 20 November 2019
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	==Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 2.5 mM Na+ and 1mM Sr2+==		==Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 2.5 mM Na+ and 1mM Sr2+==
	<StructureSection load='5jdl' size='340' side='right' caption='[[5jdl]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5jdl' size='340' side='right'caption='[[5jdl]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jdl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JDL FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jdl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JDL FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5jdl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jdl" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Sodium-calcium exchanger\|Sodium-calcium exchanger]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Metja]]		[[Category: Metja]]
	[[Category: Faraldo-Gomez, J D]]		[[Category: Faraldo-Gomez, J D]]

OCA at 17:54, 15 November 2017

2017-11-15T17:54:37Z

← Older revision		Revision as of 17:54, 15 November 2017
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	<StructureSection load='5jdl' size='340' side='right' caption='[[5jdl]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5jdl' size='340' side='right' caption='[[5jdl]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jdl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JDL FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jdl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JDL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MYS:PENTADECANE'>MYS</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MYS:PENTADECANE'>MYS</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jdq\|5jdq]], [[5jdn\|5jdn]], [[5jdm\|5jdm]], [[5jdh\|5jdh]], [[5jdg\|5jdg]], [[5jdf\|5jdf]], [[5hwx\|5hwx]], [[5hwy\|5hwy]], [[5hxc\|5hxc]], [[5hxe\|5hxe]], [[5hxh\|5hxh]], [[5hxr\|5hxr]], [[5hxs\|5hxs]], [[5hya\|5hya]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jdq\|5jdq]], [[5jdn\|5jdn]], [[5jdm\|5jdm]], [[5jdh\|5jdh]], [[5jdg\|5jdg]], [[5jdf\|5jdf]], [[5hwx\|5hwx]], [[5hwy\|5hwy]], [[5hxc\|5hxc]], [[5hxe\|5hxe]], [[5hxh\|5hxh]], [[5hxr\|5hxr]], [[5hxs\|5hxs]], [[5hya\|5hya]]</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=5jdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdl OCA], [http://pdbe.org/5jdl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jdl RCSB], [http://www.ebi.ac.uk/pdbsum/5jdl PDBsum]</span></td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ0091 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</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=5jdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdl OCA], [http://pdbe.org/5jdl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jdl RCSB], [http://www.ebi.ac.uk/pdbsum/5jdl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jdl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Metja]]
	[[Category: Faraldo-Gomez, J D]]		[[Category: Faraldo-Gomez, J D]]
	[[Category: Jiang, Y X]]		[[Category: Jiang, Y X]]

OCA at 08:39, 1 June 2016

2016-06-01T08:39:15Z

← Older revision		Revision as of 08:39, 1 June 2016
Line 10:		Line 10:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	~~Sodium/calcium (~~Na(+)/~~Ca(2~~+)) exchangers ~~(NCX) are~~ membrane ~~transporters that~~ play ~~an essential~~ role in ~~maintaining the~~ homeostasis of ~~cytosolic Ca(2+) for cell signaling. We demonstrated the Na(+)/Ca(2+)-~~exchange ~~function~~ of ~~an NCX~~ from Methanococcus jannaschii (NCX_Mj) and ~~report its 1.9 angstrom crystal structure~~ in an ~~outward-facing conformation~~. ~~Containing 10 transmembrane helices,~~ the ~~two halves~~ of ~~NCX_Mj share a similar structure with opposite orientation. Four ion-binding sites cluster at~~ the ~~center of~~ the ~~protein~~: ~~one specific for Ca(2+) and three that likely bind~~ Na(+~~). Two passageways allow for Na(~~+) and ~~Ca(2+)~~ access to the ~~central~~ ion-~~binding sites from~~ the ~~extracellular side~~. ~~Based on~~ the ~~symmetry of NCX_Mj and its ability~~ to ~~catalyze bidirectional~~ ion~~-exchange reactions~~, ~~we propose a structure model for~~ the ~~inward-facing NCX_Mj~~.		Na+/Ca2+ exchangers use the Na+ electrochemical gradient across the plasma membrane to extrude intracellular Ca2+ and play a central role in Ca2+ homeostasis. Here, we elucidate their mechanisms of extracellular ion recognition and exchange through a structural analysis of the exchanger from Methanococcus jannaschii (NCX_Mj) bound to Na+, Ca2+ or Sr2+ in various occupancies and in an apo state. This analysis defines the binding mode and relative affinity of these ions, establishes the structural basis for the anticipated 3:1 Na+/Ca2+-exchange stoichiometry and reveals the conformational changes at the onset of the alternating-access transport mechanism. An independent analysis of the dynamics and conformational free-energy landscape of NCX_Mj in different ion-occupancy states, based on enhanced-sampling molecular dynamics simulations, demonstrates that the crystal structures reflect mechanistically relevant, interconverting conformations. These calculations also reveal the mechanism by which the outward-to-inward transition is controlled by the ion occupancy, thereby explaining the emergence of strictly coupled Na+/Ca2+ antiport.

	~~Structural insight into the~~ ion-~~exchange mechanism of the~~ sodium/calcium exchanger.,Liao J, ~~Li H~~, ~~Zeng W~~, ~~Sauer DB~~, ~~Belmares R~~, Jiang Y ~~Science~~. ~~2012 Feb~~ 10~~;335(6069):686-90~~. PMID:~~22323814~~<ref>PMID:~~22323814~~</ref>		Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger.,Liao J, Marinelli F, Lee C, Huang Y, Faraldo-Gomez JD, Jiang Y Nat Struct Mol Biol. 2016 May 16. doi: 10.1038/nsmb.3230. PMID:27183196<ref>PMID:27183196</ref>

	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>

OCA at 16:59, 15 May 2016

2016-05-15T16:59:10Z

← Older revision		Revision as of 16:59, 15 May 2016
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	~~'''Unreleased structure'''~~

	~~The entry~~ 5jdl is ~~ON HOLD until Paper~~ Publication		==Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 2.5 mM Na+ and 1mM Sr2+==
			<StructureSection load='5jdl' size='340' side='right' caption='[[5jdl]], [[Resolution\|resolution]] 2.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[5jdl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JDL FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MYS:PENTADECANE'>MYS</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5jdq\|5jdq]], [[5jdn\|5jdn]], [[5jdm\|5jdm]], [[5jdh\|5jdh]], [[5jdg\|5jdg]], [[5jdf\|5jdf]], [[5hwx\|5hwx]], [[5hwy\|5hwy]], [[5hxc\|5hxc]], [[5hxe\|5hxe]], [[5hxh\|5hxh]], [[5hxr\|5hxr]], [[5hxs\|5hxs]], [[5hya\|5hya]]</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=5jdl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdl OCA], [http://pdbe.org/5jdl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jdl RCSB], [http://www.ebi.ac.uk/pdbsum/5jdl PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Sodium/calcium (Na(+)/Ca(2+)) exchangers (NCX) are membrane transporters that play an essential role in maintaining the homeostasis of cytosolic Ca(2+) for cell signaling. We demonstrated the Na(+)/Ca(2+)-exchange function of an NCX from Methanococcus jannaschii (NCX_Mj) and report its 1.9 angstrom crystal structure in an outward-facing conformation. Containing 10 transmembrane helices, the two halves of NCX_Mj share a similar structure with opposite orientation. Four ion-binding sites cluster at the center of the protein: one specific for Ca(2+) and three that likely bind Na(+). Two passageways allow for Na(+) and Ca(2+) access to the central ion-binding sites from the extracellular side. Based on the symmetry of NCX_Mj and its ability to catalyze bidirectional ion-exchange reactions, we propose a structure model for the inward-facing NCX_Mj.

	~~Authors:~~ Liao, J., Jiang, Y.~~X., Faraldo~~-~~Gomez, J.D~~.		Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger.,Liao J, Li H, Zeng W, Sauer DB, Belmares R, Jiang Y Science. 2012 Feb 10;335(6069):686-90. PMID:22323814<ref>PMID:22323814</ref>

	~~Description: Structural mechanisms~~ of ~~extracellular ion exchange and induced binding~~-~~site occlusion in the sodium~~-~~calcium exchanger NCX_Mj soaked with 2.5 mM Na+ and 1mM Sr2+~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased Structures~~]]		</div>
			<div class="pdbe-citations 5jdl" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Faraldo-Gomez, J D]]
			[[Category: Jiang, Y X]]
	[[Category: Liao, J]]		[[Category: Liao, J]]
	[[Category: ~~Faraldo-Gomez, J.D~~]]		[[Category: Calcium signalling]]
	[[Category: ~~Jiang, Y.X~~]]		[[Category: Induced conformational change]]
			[[Category: Membrane protein]]
			[[Category: Membrane transporter]]
			[[Category: Na+/ca2+ exchange]]

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

2016-05-11T01:54:01Z

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

← Older revision	Revision as of 01:54, 11 May 2016
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5jdl is ON HOLD until Paper Publication Authors: Liao, J., Jiang, Y.X., Faraldo-Gomez, J.D. Description: Structural mechanisms of extracellular ion...

2016-05-11T01:54:00Z

New page: '''Unreleased structure''' The entry 5jdl is ON HOLD until Paper Publication Authors: Liao, J., Jiang, Y.X., Faraldo-Gomez, J.D. Description: Structural mechanisms of extracellular ion...

New page

'''Unreleased structure'''

The entry 5jdl is ON HOLD until Paper Publication

Authors: Liao, J., Jiang, Y.X., Faraldo-Gomez, J.D.

Description: Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 2.5 mM Na+ and 1mM Sr2+
[[Category: Unreleased Structures]]
[[Category: Liao, J]]
[[Category: Faraldo-Gomez, J.D]]
[[Category: Jiang, Y.X]]