6sqg - Revision history

OCA at 12:45, 24 January 2024

OCA — Wed, 24 Jan 2024 12:45:52 GMT

←Older revision		Revision as of 12:45, 24 January 2024
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	<StructureSection load='6sqg' size='340' side='right'caption='[[6sqg]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6sqg' size='340' side='right'caption='[[6sqg]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6sqg]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Organic_lake_phycodnavirus~~ Organic ~~lake~~ phycodnavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6SQG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6sqg]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Organic_Lake_phycodnavirus Organic Lake phycodnavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SQG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=OLB:(2S)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLB</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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]] 1.9Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">162286292 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=938083 Organic Lake phycodnavirus])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=OLB:(2S)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLB</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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=6sqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqg OCA], [~~http~~://pdbe.org/6sqg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6sqg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6sqg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqg 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=6sqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqg OCA], [https://pdbe.org/6sqg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sqg RCSB], [https://www.ebi.ac.uk/pdbsum/6sqg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/F2Y2Z0_9PHYC F2Y2Z0_9PHYC]
	<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 6sqg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6sqg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Rhodopsin 3D structures\|Rhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Organic ~~lake~~ phycodnavirus]]	+	[[Category: Organic Lake phycodnavirus]]
-	[[Category: Astashkin, R]]	+	[[Category: Astashkin R]]
-	[[Category: Bourenkov, G]]	+	[[Category: Bourenkov G]]
-	[[Category: Bratanov, D]]	+	[[Category: Bratanov D]]
-	[[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: Popov, A]]	+	[[Category: Popov A]]
-	~~[[Category: Ion transport]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Pentamer]]~~	+
-	~~[[Category: Proton pump]]~~	+
-	~~[[Category: Rhodopsin]]~~	+
-	~~[[Category: Viral rhodopsin~~]]	+

OCA at 11:51, 13 November 2019

OCA — Wed, 13 Nov 2019 11:51:44 GMT

←Older revision		Revision as of 11:51, 13 November 2019
Line 3:		Line 3:
	<StructureSection load='6sqg' size='340' side='right'caption='[[6sqg]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6sqg' size='340' side='right'caption='[[6sqg]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6sqg]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SQG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6sqg]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Organic_lake_phycodnavirus Organic lake phycodnavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SQG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=OLB:(2S)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLB</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=OLB:(2S)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLB</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">162286292 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=938083 Organic Lake phycodnavirus])</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=6sqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqg OCA], [http://pdbe.org/6sqg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sqg RCSB], [http://www.ebi.ac.uk/pdbsum/6sqg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqg 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=6sqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqg OCA], [http://pdbe.org/6sqg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sqg RCSB], [http://www.ebi.ac.uk/pdbsum/6sqg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqg ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Recently, two groups of rhodopsin genes were identified in large double-stranded DNA viruses. The structure and function of viral rhodopsins are unknown. We present functional characterization and high-resolution structure of an Organic Lake Phycodnavirus rhodopsin II (OLPVRII) of group 2. It forms a pentamer, with a symmetrical, bottle-like central channel with the narrow vestibule in the cytoplasmic part covered by a ring of 5 arginines, whereas 5 phenylalanines form a hydrophobic barrier in its exit. The proton donor E42 is placed in the helix B. The structure is unique among the known rhodopsins. Structural and functional data and molecular dynamics suggest that OLPVRII might be a light-gated pentameric ion channel analogous to pentameric ligand-gated ion channels, however, future patch clamp experiments should prove this directly. The data shed light on a fundamentally distinct branch of rhodopsins and may contribute to the understanding of virus-host interactions in ecologically important marine protists.
		+
		+	Unique structure and function of viral rhodopsins.,Bratanov D, Kovalev K, Machtens JP, Astashkin R, Chizhov I, Soloviov D, Volkov D, Polovinkin V, Zabelskii D, Mager T, Gushchin I, Rokitskaya T, Antonenko Y, Alekseev A, Shevchenko V, Yutin N, Rosselli R, Baeken C, Borshchevskiy V, Bourenkov G, Popov A, Balandin T, Buldt G, Manstein DJ, Rodriguez-Valera F, Fahlke C, Bamberg E, Koonin E, Gordeliy V Nat Commun. 2019 Oct 30;10(1):4939. doi: 10.1038/s41467-019-12718-0. PMID:31666521<ref>PMID:31666521</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6sqg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Organic lake phycodnavirus]]
	[[Category: Astashkin, R]]		[[Category: Astashkin, R]]
	[[Category: Bourenkov, G]]		[[Category: Bourenkov, G]]

OCA at 06:52, 6 November 2019

OCA — Wed, 06 Nov 2019 06:52:17 GMT

←Older revision		Revision as of 06:52, 6 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6sqg ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of viral rhodopsin OLPVRII==
-		+	<StructureSection load='6sqg' size='340' side='right'caption='[[6sqg]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6sqg]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SQG FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=OLB:(2S)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLB</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6sqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sqg OCA], [http://pdbe.org/6sqg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sqg RCSB], [http://www.ebi.ac.uk/pdbsum/6sqg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sqg ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Astashkin, R]]
		+	[[Category: Bourenkov, G]]
		+	[[Category: Bratanov, D]]
		+	[[Category: Gordeliy, V]]
		+	[[Category: Gushchin, I]]
		+	[[Category: Kovalev, K]]
		+	[[Category: Polovinkin, V]]
		+	[[Category: Popov, A]]
		+	[[Category: Ion transport]]
		+	[[Category: Membrane protein]]
		+	[[Category: Pentamer]]
		+	[[Category: Proton pump]]
		+	[[Category: Rhodopsin]]
		+	[[Category: Viral rhodopsin]]

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

OCA — Wed, 02 Oct 2019 07:36:09 GMT

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

←Older revision

Revision as of 07:36, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6sqg is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Oct 2019 07:36:07 GMT

New page: '''Unreleased structure''' The entry 6sqg is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6sqg is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]