6yc2 - Revision history

OCA at 13:23, 24 January 2024

OCA — Wed, 24 Jan 2024 13:23:43 GMT

←Older revision		Revision as of 13:23, 24 January 2024
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	<StructureSection load='6yc2' size='340' side='right'caption='[[6yc2]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6yc2' size='340' side='right'caption='[[6yc2]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yc2]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cip_108743 Cip 108743~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YC2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YC2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yc2]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Dokdonia_eikasta Dokdonia eikasta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YC2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YC2 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ALA:ALANINE'>ALA</scene>~~, ~~<scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=OLC:(2R)-~~2~~,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</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]] 2.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=LYR:N~6~-[(2Z,4E,6E,8E)-3,7-DIMETHYL-9-(2,6,6-TRIMETHYLCYCLOHEX-1-EN-1-YL)NONA-2,4,6,8-TETRAENYL]LYSINE'>LYR</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=LYR:N~6~-[(2Z,4E,6E,8E)-3,7-DIMETHYL-9-(2,6,6-TRIMETHYLCYCLOHEX-1-EN-1-YL)NONA-2,4,6,8-TETRAENYL]LYSINE'>LYR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">NaR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=308116 CIP 108743])~~</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=6yc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yc2 OCA], [https://pdbe.org/6yc2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yc2 RCSB], [https://www.ebi.ac.uk/pdbsum/6yc2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yc2 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=6yc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yc2 OCA], [~~http~~://pdbe.org/6yc2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yc2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yc2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yc2 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/N0DKS8_9FLAO N0DKS8_9FLAO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6yc2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6yc2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Rhodopsin 3D structures\|Rhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cip 108743~~]]	+	[[Category: Dokdonia eikasta]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gordeliy, V]]	+	[[Category: Gordeliy V]]
-	[[Category: Gushchin, I]]	+	[[Category: Gushchin I]]
-	[[Category: Kovalev, K]]	+	[[Category: Kovalev K]]
-	~~[[Category: Intermediate state]]~~	+
-	~~[[Category: Ion pumping]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Retinal]]~~	+
-	~~[[Category: Rhodopsin]]~~	+
-	~~[[Category: Sodium pump~~]]	+

OCA at 06:03, 13 May 2020

OCA — Wed, 13 May 2020 06:03:39 GMT

←Older revision		Revision as of 06:03, 13 May 2020
Line 3:		Line 3:
	<StructureSection load='6yc2' size='340' side='right'caption='[[6yc2]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6yc2' size='340' side='right'caption='[[6yc2]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yc2]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YC2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YC2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yc2]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Cip_108743 Cip 108743]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YC2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YC2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LYR:N~6~-[(2Z,4E,6E,8E)-3,7-DIMETHYL-9-(2,6,6-TRIMETHYLCYCLOHEX-1-EN-1-YL)NONA-2,4,6,8-TETRAENYL]LYSINE'>LYR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LYR:N~6~-[(2Z,4E,6E,8E)-3,7-DIMETHYL-9-(2,6,6-TRIMETHYLCYCLOHEX-1-EN-1-YL)NONA-2,4,6,8-TETRAENYL]LYSINE'>LYR</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NaR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=308116 CIP 108743])</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=6yc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yc2 OCA], [http://pdbe.org/6yc2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yc2 RCSB], [http://www.ebi.ac.uk/pdbsum/6yc2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yc2 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=6yc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yc2 OCA], [http://pdbe.org/6yc2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yc2 RCSB], [http://www.ebi.ac.uk/pdbsum/6yc2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yc2 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The light-driven sodium-pumping rhodopsin KR2 from Krokinobacter eikastus is the only non-proton cation active transporter with demonstrated potential for optogenetics. However, the existing structural data on KR2 correspond exclusively to its ground state, and show no sodium inside the protein, which hampers the understanding of sodium-pumping mechanism. Here we present crystal structure of the O-intermediate of the physiologically relevant pentameric form of KR2 at the resolution of 2.1 A, revealing a sodium ion near the retinal Schiff base, coordinated by N112 and D116 of the characteristic NDQ triad. We also obtained crystal structures of D116N and H30A variants, conducted metadynamics simulations and measured pumping activities of putative pathway mutants to demonstrate that sodium release likely proceeds alongside Q78 towards the structural sodium ion bound between KR2 protomers. Our findings highlight the importance of pentameric assembly for sodium pump function, and may be used for rational engineering of enhanced optogenetic tools.
		+
		+	Molecular mechanism of light-driven sodium pumping.,Kovalev K, Astashkin R, Gushchin I, Orekhov P, Volkov D, Zinovev E, Marin E, Rulev M, Alekseev A, Royant A, Carpentier P, Vaganova S, Zabelskii D, Baeken C, Sergeev I, Balandin T, Bourenkov G, Carpena X, Boer R, Maliar N, Borshchevskiy V, Buldt G, Bamberg E, Gordeliy V Nat Commun. 2020 May 1;11(1):2137. doi: 10.1038/s41467-020-16032-y. PMID:32358514<ref>PMID:32358514</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yc2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cip 108743]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Gordeliy, V]]		[[Category: Gordeliy, V]]

OCA at 07:04, 8 April 2020

OCA — Wed, 08 Apr 2020 07:04:20 GMT

←Older revision		Revision as of 07:04, 8 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6yc2 is ON HOLD until Paper Publication~~	+	==Crystal structure of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0==
-		+	<StructureSection load='6yc2' size='340' side='right'caption='[[6yc2]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~Authors: Kovalev, K., Gushchin, I., Gordeliy, V.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6yc2]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YC2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YC2 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</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=LYR:N~6~-[(2Z,4E,6E,8E)-3,7-DIMETHYL-9-(2,6,6-TRIMETHYLCYCLOHEX-1-EN-1-YL)NONA-2,4,6,8-TETRAENYL]LYSINE'>LYR</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=6yc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yc2 OCA], [http://pdbe.org/6yc2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yc2 RCSB], [http://www.ebi.ac.uk/pdbsum/6yc2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yc2 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Gordeliy, V]]		[[Category: Gordeliy, V]]
	[[Category: Gushchin, I]]		[[Category: Gushchin, I]]
	[[Category: Kovalev, K]]		[[Category: Kovalev, K]]
		+	[[Category: Intermediate state]]
		+	[[Category: Ion pumping]]
		+	[[Category: Membrane protein]]
		+	[[Category: Retinal]]
		+	[[Category: Rhodopsin]]
		+	[[Category: Sodium pump]]

OCA: Protected "6yc2" [edit=sysop:move=sysop]

OCA — Fri, 27 Mar 2020 08:37:16 GMT

Protected "6yc2" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:37, 27 March 2020

OCA: New page: '''Unreleased structure''' The entry 6yc2 is ON HOLD until Paper Publication Authors: Kovalev, K., Gushchin, I., Gordeliy, V. Description: Crystal structure of the light-driven sodium ...

OCA — Fri, 27 Mar 2020 08:37:15 GMT

New page: '''Unreleased structure''' The entry 6yc2 is ON HOLD until Paper Publication Authors: Kovalev, K., Gushchin, I., Gordeliy, V. Description: Crystal structure of the light-driven sodium ...

New page

'''Unreleased structure'''

The entry 6yc2 is ON HOLD until Paper Publication

Authors: Kovalev, K., Gushchin, I., Gordeliy, V.

Description: Crystal structure of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0
[[Category: Unreleased Structures]]
[[Category: Gordeliy, V]]
[[Category: Gushchin, I]]
[[Category: Kovalev, K]]