6xyt - Revision history

OCA at 13:15, 24 January 2024

OCA — Wed, 24 Jan 2024 13:15:33 GMT

←Older revision		Revision as of 13:15, 24 January 2024
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	<StructureSection load='6xyt' size='340' side='right'caption='[[6xyt]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6xyt' size='340' side='right'caption='[[6xyt]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xyt]] 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=6XYT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6XYT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xyt]] 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=6XYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XYT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~"><~~scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'~~>~~BOG~~</~~scene~~>, <~~scene name~~='~~pdbligand=GOL:GLYCEROL~~'>~~GOL~~<~~/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]] 2.1Å</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=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6xyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xyt OCA], [https://pdbe.org/6xyt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xyt RCSB], [https://www.ebi.ac.uk/pdbsum/6xyt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xyt 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=6xyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xyt OCA], [~~http~~://pdbe.org/6xyt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6xyt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6xyt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6xyt 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 6xyt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6xyt" 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 10:50, 17 June 2020

OCA — Wed, 17 Jun 2020 10:50:38 GMT

←Older revision		Revision as of 10:50, 17 June 2020
Line 3:		Line 3:
	<StructureSection load='6xyt' size='340' side='right'caption='[[6xyt]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6xyt' size='340' side='right'caption='[[6xyt]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xyt]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XYT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6XYT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xyt]] 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=6XYT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XYT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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='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=6xyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xyt OCA], [http://pdbe.org/6xyt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xyt RCSB], [http://www.ebi.ac.uk/pdbsum/6xyt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xyt ProSAT]</span></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=6xyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xyt OCA], [http://pdbe.org/6xyt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xyt RCSB], [http://www.ebi.ac.uk/pdbsum/6xyt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xyt 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 6xyt" 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: Protected "6xyt" [edit=sysop:move=sysop]

OCA — Thu, 13 Feb 2020 04:31:53 GMT

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

←Older revision

Revision as of 04:31, 13 February 2020

OCA: New page: ==Crystal structure of the O-state of the light-driven sodium pump KR2 in the pentameric form, pH 8.0== == Structural highlights ==
<table><tr><td colspan='2'>[[6xyt]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XYT OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6XYT FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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">[[Non-Standard_Residue|NonStd Res:]]</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">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6xyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xyt OCA], [http://pdbe.org/6xyt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xyt RCSB], [http://www.ebi.ac.uk/pdbsum/6xyt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xyt ProSAT]</td></tr>
</table>
TOC
</StructureSection>
[[Category: Large Structures]]
[[Category: Gordeliy, V]]
[[Category: Gushchin, I]]
[[Category: Kovalev, K]]
[[Category: Intermediate state]]
[[Category: Ion pumping]]
[[Category: Membrane protein]]
[[Category: Retinal]]
[[Category: Rhodopsin]]
[[Category: Sodium pump]]