3vvk - Revision history

OCA at 12:39, 8 November 2023

2023-11-08T12:39:25Z

←Older revision		Revision as of 12:39, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vvk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Natronomonas_pharaonis Natronomonas pharaonis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VVK FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vvk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Natronomonas_pharaonis Natronomonas pharaonis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VVK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</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]] 2.3Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a7k\|3a7k]], [[3qbi\|3qbi]], [[3qbk\|3qbk]], [[3qbl\|3qbl]], [[3abw\|3abw]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</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'>[https://proteopedia.org/fgij/fg.htm?mol=3vvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvk OCA], [https://pdbe.org/3vvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vvk RCSB], [https://www.ebi.ac.uk/pdbsum/3vvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vvk 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=3vvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvk OCA], [https://pdbe.org/3vvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vvk RCSB], [https://www.ebi.ac.uk/pdbsum/3vvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vvk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BACH_NATPH BACH_NATPH] Light-driven anion pump. Binding affinity for the anions is in the order, bromide > chloride > nitrate > azide > bromate and binding is pH dependent.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Natronomonas pharaonis]]		[[Category: Natronomonas pharaonis]]
-	[[Category: Kouyama, T]]	+	[[Category: Kouyama T]]
-	[[Category: Nakanishi, T]]	+	[[Category: Nakanishi T]]
-	~~[[Category: Azide-bound purple form]]~~	+
-	~~[[Category: Chloride-bound purple form]]~~	+
-	~~[[Category: Light-driven chloride ion pump]]~~	+
-	~~[[Category: Light-driven proton pump]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Seven-transmembrane-retinylidene protein~~]]	+

OCA at 19:06, 27 July 2022

2022-07-27T19:06:28Z

←Older revision		Revision as of 19:06, 27 July 2022
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	==An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin==		==An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin==
-	<StructureSection load='3vvk' size='340' side='right' caption='[[3vvk]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3vvk' size='340' side='right'caption='[[3vvk]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vvk]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Natronomonas_pharaonis Natronomonas pharaonis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VVK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vvk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Natronomonas_pharaonis Natronomonas pharaonis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VVK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</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" id="ligandDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a7k\|3a7k]], [[3qbi\|3qbi]], [[3qbk\|3qbk]], [[3qbl\|3qbl]], [[3abw\|3abw]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a7k\|3a7k]], [[3qbi\|3qbi]], [[3qbk\|3qbk]], [[3qbl\|3qbl]], [[3abw\|3abw]]</div></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=3vvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvk OCA], [~~http~~://pdbe.org/3vvk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vvk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vvk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vvk 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=3vvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvk OCA], [https://pdbe.org/3vvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vvk RCSB], [https://www.ebi.ac.uk/pdbsum/3vvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vvk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]	+	*[[Bacteriorhodopsin 3D structures\|Bacteriorhodopsin 3D structures]]
-	*[[Rhodopsin\|Rhodopsin]]	+	*[[Rhodopsin 3D structures\|Rhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Natronomonas pharaonis]]		[[Category: Natronomonas pharaonis]]
	[[Category: Kouyama, T]]		[[Category: Kouyama, T]]

OCA at 14:21, 11 August 2016

2016-08-11T14:21:45Z

←Older revision		Revision as of 14:21, 11 August 2016
Line 1:		Line 1:
		+
	==An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin==		==An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin==
	<StructureSection load='3vvk' size='340' side='right' caption='[[3vvk]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3vvk' size='340' side='right' caption='[[3vvk]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</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=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a7k\|3a7k]], [[3qbi\|3qbi]], [[3qbk\|3qbk]], [[3qbl\|3qbl]], [[3abw\|3abw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a7k\|3a7k]], [[3qbi\|3qbi]], [[3qbk\|3qbk]], [[3qbl\|3qbl]], [[3abw\|3abw]]</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=3vvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vvk RCSB], [http://www.ebi.ac.uk/pdbsum/3vvk PDBsum]</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=3vvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvk OCA], [http://pdbe.org/3vvk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vvk RCSB], [http://www.ebi.ac.uk/pdbsum/3vvk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vvk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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>
	</div>		</div>
		+	<div class="pdbe-citations 3vvk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 09:25, 4 January 2015

2015-01-04T09:25:23Z

←Older revision		Revision as of 09:25, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3vvk\| PDB=3vvk \| SCENE= }}~~	+	==An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin==
-	===An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin===	+	<StructureSection load='3vvk' size='340' side='right' caption='[[3vvk]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23442859}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3vvk]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Natronomonas_pharaonis Natronomonas pharaonis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VVK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3a7k\|3a7k]], [[3qbi\|3qbi]], [[3qbk\|3qbk]], [[3qbl\|3qbl]], [[3abw\|3abw]]</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=3vvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vvk RCSB], [http://www.ebi.ac.uk/pdbsum/3vvk PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Halorhodopsin from Natronomonas pharaonis (pHR), a retinylidene protein that functions as a light-driven chloride ion pump, is converted into a proton pump in the presence of azide ion. To clarify this conversion, we investigated light-induced structural changes in pHR using a C2 crystal that was prepared in the presence of Cl(-) and subsequently soaked in a solution containing azide ion. When the pHR-azide complex was illuminated at pH 9, a profound outward movement ( approximately 4 A) of the cytoplasmic half of helix F was observed in a subunit with the EF loop facing an open space. This movement created a long water channel between the retinal Schiff base and the cytoplasmic surface, along which a proton could be transported. Meanwhile, the middle moiety of helix C moved inward, leading to shrinkage of the primary anion-binding site (site I), and the azide molecule in site I was expelled out to the extracellular medium. The results suggest that the cytoplasmic half of helix F and the middle moiety of helix C act as different types of valves for active proton transport.

-	~~==About this Structure==~~	+	Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide.,Nakanishi T, Kanada S, Murakami M, Ihara K, Kouyama T Biophys J. 2013 Jan 22;104(2):377-85. doi: 10.1016/j.bpj.2012.12.018. PMID:23442859<ref>PMID:23442859</ref>
-	~~[[3vvk]] is a 6 chain structure~~ with ~~sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Natronomonas_pharaonis Natronomonas pharaonis]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3VVK OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:023442859</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]
		+	*[[Rhodopsin\|Rhodopsin]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Natronomonas pharaonis]]		[[Category: Natronomonas pharaonis]]
-	[[Category: Kouyama, T.]]	+	[[Category: Kouyama, T]]
-	[[Category: Nakanishi, T.]]	+	[[Category: Nakanishi, T]]
	[[Category: Azide-bound purple form]]		[[Category: Azide-bound purple form]]
	[[Category: Chloride-bound purple form]]		[[Category: Chloride-bound purple form]]

OCA at 13:49, 19 June 2013

2013-06-19T13:49:17Z

←Older revision		Revision as of 13:49, 19 June 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_3vvk\| PDB=3vvk \| SCENE= }}
		+	===An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin===
		+	{{ABSTRACT_PUBMED_23442859}}

-	~~The entry~~ 3vvk is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[3vvk]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Natronomonas_pharaonis Natronomonas pharaonis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVK OCA].

-	~~Authors~~: Kouyama, T., Nakanishi, T.	+	==Reference==
-		+	<ref group="xtra">PMID:023442859</ref><references group="xtra"/><references/>
-	~~Description~~: ~~An M-like Reaction State of the azide~~-bound purple form ~~of pharaonis halorhodopsin~~	+	[[Category: Natronomonas pharaonis]]
		+	[[Category: Kouyama, T.]]
		+	[[Category: Nakanishi, T.]]
		+	[[Category: Azide-bound purple form]]
		+	[[Category: Chloride-bound purple form]]
		+	[[Category: Light-driven chloride ion pump]]
		+	[[Category: Light-driven proton pump]]
		+	[[Category: Membrane protein]]
		+	[[Category: Seven-transmembrane-retinylidene protein]]

OCA at 13:49, 28 November 2012

2012-11-28T13:49:53Z

←Older revision		Revision as of 13:49, 28 November 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3vvk is ON HOLD	+	The entry 3vvk is ON HOLD until Paper Publication

	Authors: Kouyama, T., Nakanishi, T.		Authors: Kouyama, T., Nakanishi, T.

	Description: An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin		Description: An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin

OCA: Protected "3vvk" [edit=sysop:move=sysop]

2012-08-01T05:15:21Z

Protected "3vvk" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:15, 1 August 2012

OCA: New page: '''Unreleased structure''' The entry 3vvk is ON HOLD Authors: Kouyama, T., Nakanishi, T. Description: An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin

2012-08-01T05:15:20Z

New page: '''Unreleased structure''' The entry 3vvk is ON HOLD Authors: Kouyama, T., Nakanishi, T. Description: An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin

New page

'''Unreleased structure'''

The entry 3vvk is ON HOLD

Authors: Kouyama, T., Nakanishi, T.

Description: An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin