6rf3 - Revision history

OCA at 12:19, 24 January 2024

2024-01-24T12:19:24Z

←Older revision		Revision as of 12:19, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6rf3' size='340' side='right'caption='[[6rf3]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6rf3' size='340' side='right'caption='[[6rf3]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rf3]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RF3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RF3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rf3]] 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=6RF3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RF3 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=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.4Å</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=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=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</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=6rf3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rf3 OCA], [~~http~~://pdbe.org/6rf3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rf3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rf3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rf3 ProSAT]</span></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=6rf3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rf3 OCA], [https://pdbe.org/6rf3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rf3 RCSB], [https://www.ebi.ac.uk/pdbsum/6rf3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rf3 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 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6rf3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6rf3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Rhodopsin 3D structures\|Rhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dokdonia eikasta]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Borshchevskiy, V]]	+	[[Category: Borshchevskiy V]]
-	[[Category: Gordeliy, V]]	+	[[Category: Gordeliy V]]
-	[[Category: Gushchin, I]]	+	[[Category: Gushchin I]]
-	[[Category: Kovalev, K]]	+	[[Category: Kovalev K]]
-	[[Category: Polovinkin, V]]	+	[[Category: Polovinkin V]]
-	~~[[Category: Ion translocation]]~~	+
-	~~[[Category: Light-driven sodium pump]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Retinal]]~~	+
-	~~[[Category: Rhodopsin~~]]	+

OCA: Protected "6rf3" [edit=sysop:move=sysop]

2019-04-24T07:15:10Z

Protected "6rf3" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:15, 24 April 2019

OCA: New page: ==Crystal structure of the potassium-pumping G263F mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0==
2019-04-24T07:15:08Z

New page: ==Crystal structure of the potassium-pumping G263F mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0== <StructureSection load='6rf3' size='340' side='right'caption...

New page

==Crystal structure of the potassium-pumping G263F mutant of the light-driven sodium pump KR2 in the pentameric form, pH 8.0==
<StructureSection load='6rf3' size='340' side='right'caption='[[6rf3]], [[Resolution|resolution]] 2.40Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6rf3]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RF3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RF3 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=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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='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=6rf3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rf3 OCA], [http://pdbe.org/6rf3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rf3 RCSB], [http://www.ebi.ac.uk/pdbsum/6rf3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rf3 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Rhodopsins are the most universal biological light-energy transducers and abundant phototrophic mechanisms that evolved on Earth and have a remarkable diversity and potential for biotechnological applications. Recently, the first sodium-pumping rhodopsin KR2 from Krokinobacter eikastus was discovered and characterized. However, the existing structures of KR2 are contradictory, and the mechanism of Na(+) pumping is not yet understood. Here, we present a structure of the cationic (non H(+)) light-driven pump at physiological pH in its pentameric form. We also present 13 atomic structures and functional data on the KR2 and its mutants, including potassium pumps, which show that oligomerization of the microbial rhodopsin is obligatory for its biological function. The studies reveal the structure of KR2 at nonphysiological low pH where it acts as a proton pump. The structure provides new insights into the mechanisms of microbial rhodopsins and opens the way to a rational design of novel cation pumps for optogenetics.

Structure and mechanisms of sodium-pumping KR2 rhodopsin.,Kovalev K, Polovinkin V, Gushchin I, Alekseev A, Shevchenko V, Borshchevskiy V, Astashkin R, Balandin T, Bratanov D, Vaganova S, Popov A, Chupin V, Buldt G, Bamberg E, Gordeliy V Sci Adv. 2019 Apr 10;5(4):eaav2671. doi: 10.1126/sciadv.aav2671. eCollection 2019, Apr. PMID:30989112<ref>PMID:30989112</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6rf3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Large Structures]]
[[Category: Borshchevskiy, V]]
[[Category: Gordeliy, V]]
[[Category: Gushchin, I]]
[[Category: Kovalev, K]]
[[Category: Polovinkin, V]]
[[Category: Ion translocation]]
[[Category: Light-driven sodium pump]]
[[Category: Membrane protein]]
[[Category: Retinal]]
[[Category: Rhodopsin]]