2z55 - Revision history

OCA at 13:21, 1 November 2023

OCA — Wed, 01 Nov 2023 13:21:51 GMT

←Older revision		Revision as of 13:21, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2z55' size='340' side='right'caption='[[2z55]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2z55' size='340' side='right'caption='[[2z55]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z55]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Halobacterium_sp.~~_aus~~-2 Halobacterium sp. ~~aus~~-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2Z55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z55]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_sp._AUS-2 Halobacterium sp. AUS-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z55 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=~~GLC~~:~~ALPHA~~-D-~~GLUCOSE~~'>~~GLC~~</scene>, <scene name='pdbligand=~~L2P~~:~~2,3~~-DI-~~PHYTANYL-GLYCEROL~~'>~~L2P~~</scene>, <scene name='pdbligand=~~RET~~:~~RETINAL'>RET</scene>~~, ~~<scene name='pdbligand=GAL:BETA~~-D-~~GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[2ei4\|2ei4]], [[1vgo\|1vgo]], [[1uaz\|1uaz]], [[1iw6\|1iw6]]~~</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=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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~~://proteopedia.org/fgij/fg.htm?mol=2z55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z55 OCA], [~~http~~://pdbe.org/2z55 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z55 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z55 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z55 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=2z55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z55 OCA], [https://pdbe.org/2z55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z55 RCSB], [https://www.ebi.ac.uk/pdbsum/2z55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z55 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BACR2_HALS2 BACR2_HALS2]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Halobacterium sp. ~~aus~~-2]]	+	[[Category: Halobacterium sp. AUS-2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kouyama, T]]	+	[[Category: Kouyama T]]
-	[[Category: Yoshimura, K]]	+	[[Category: Yoshimura K]]
-	~~[[Category: Bacterioruberin]]~~	+
-	~~[[Category: Retinal protein]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 11:57, 29 July 2020

OCA — Wed, 29 Jul 2020 11:57:55 GMT

←Older revision		Revision as of 11:57, 29 July 2020
Line 1:		Line 1:

	==Bacterioruberin in the trimeric structure of archaerhodopsin-2==		==Bacterioruberin in the trimeric structure of archaerhodopsin-2==
-	<StructureSection load='2z55' size='340' side='right' caption='[[2z55]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='2z55' size='340' side='right'caption='[[2z55]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z55]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_sp._aus-2 Halobacterium sp. aus-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z55]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_sp._aus-2 Halobacterium sp. aus-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2Z55 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=~~GAL~~:~~BETA~~-D-~~GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=~~GLC~~:~~ALPHA~~-D-~~GLUCOSE~~'>~~GLC~~</scene>, <scene name='pdbligand=~~L2P~~:~~2,3-DI-PHYTANYL-GLYCEROL~~'>~~L2P~~</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA~~-D-~~MANNOSE~~'>~~MAN~~</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ei4\|2ei4]], [[1vgo\|1vgo]], [[1uaz\|1uaz]], [[1iw6\|1iw6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ei4\|2ei4]], [[1vgo\|1vgo]], [[1uaz\|1uaz]], [[1iw6\|1iw6]]</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=2z55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z55 OCA], [http://pdbe.org/2z55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z55 RCSB], [http://www.ebi.ac.uk/pdbsum/2z55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z55 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=2z55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z55 OCA], [http://pdbe.org/2z55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z55 RCSB], [http://www.ebi.ac.uk/pdbsum/2z55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z55 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 29:		Line 29:

	==See Also==		==See Also==
-	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]	+	*[[Bacteriorhodopsin 3D structures\|Bacteriorhodopsin 3D structures]]
-	*[[Rhodopsin\|Rhodopsin]]	+	*[[Rhodopsin 3D structures\|Rhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Halobacterium sp. aus-2]]		[[Category: Halobacterium sp. aus-2]]
		+	[[Category: Large Structures]]
	[[Category: Kouyama, T]]		[[Category: Kouyama, T]]
	[[Category: Yoshimura, K]]		[[Category: Yoshimura, K]]

OCA at 09:21, 17 October 2018

OCA — Wed, 17 Oct 2018 09:21:42 GMT

←Older revision		Revision as of 09:21, 17 October 2018
Line 1:		Line 1:
		+
	==Bacterioruberin in the trimeric structure of archaerhodopsin-2==		==Bacterioruberin in the trimeric structure of archaerhodopsin-2==
	<StructureSection load='2z55' size='340' side='right' caption='[[2z55]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2z55' size='340' side='right' caption='[[2z55]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z55]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Hals2 Hals2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z55]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_sp._aus-2 Halobacterium sp. aus-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z55 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=~~GLC~~:~~ALPHA~~-D-~~GLUCOSE~~'>~~GLC~~</scene>, <scene name='pdbligand=~~L2P~~:~~2,3~~-DI-~~PHYTANYL-GLYCEROL~~'>~~L2P~~</scene>, <scene name='pdbligand=~~RET~~:~~RETINAL~~'>~~RET~~</scene>, <scene name='pdbligand=~~GAL~~:~~BETA~~-D-~~GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA-D-MANNOSE~~'>~~MAN~~</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=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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">[[2ei4\|2ei4]], [[1vgo\|1vgo]], [[1uaz\|1uaz]], [[1iw6\|1iw6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ei4\|2ei4]], [[1vgo\|1vgo]], [[1uaz\|1uaz]], [[1iw6\|1iw6]]</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=2z55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z55 OCA], [http://pdbe.org/2z55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z55 RCSB], [http://www.ebi.ac.uk/pdbsum/2z55 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=2z55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z55 OCA], [http://pdbe.org/2z55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z55 RCSB], [http://www.ebi.ac.uk/pdbsum/2z55 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z55 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z5/2z55_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z5/2z55_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hals2~~]]	+	[[Category: Halobacterium sp. aus-2]]
	[[Category: Kouyama, T]]		[[Category: Kouyama, T]]
	[[Category: Yoshimura, K]]		[[Category: Yoshimura, K]]

OCA at 03:25, 10 February 2016

OCA — Wed, 10 Feb 2016 03:25:19 GMT

←Older revision		Revision as of 03:25, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='2z55' size='340' side='right' caption='[[2z55]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2z55' size='340' side='right' caption='[[2z55]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z55]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Archaea Archaea~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z55 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z55]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hals2 Hals2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z55 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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ei4\|2ei4]], [[1vgo\|1vgo]], [[1uaz\|1uaz]], [[1iw6\|1iw6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ei4\|2ei4]], [[1vgo\|1vgo]], [[1uaz\|1uaz]], [[1iw6\|1iw6]]</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=2z55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z55 RCSB], [http://www.ebi.ac.uk/pdbsum/2z55 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=2z55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z55 OCA], [http://pdbe.org/2z55 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z55 RCSB], [http://www.ebi.ac.uk/pdbsum/2z55 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z55 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 25:
	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 2z55" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Archaea~~]]	+	[[Category: Hals2]]
	[[Category: Kouyama, T]]		[[Category: Kouyama, T]]
	[[Category: Yoshimura, K]]		[[Category: Yoshimura, K]]

OCA at 11:27, 25 December 2014

OCA — Thu, 25 Dec 2014 11:27:58 GMT

←Older revision		Revision as of 11:27, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z55]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaea Archaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z55 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z55]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaea Archaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z55 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene><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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ei4\|2ei4]], [[1vgo\|1vgo]], [[1uaz\|1uaz]], [[1iw6\|1iw6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ei4\|2ei4]], [[1vgo\|1vgo]], [[1uaz\|1uaz]], [[1iw6\|1iw6]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z55 RCSB], [http://www.ebi.ac.uk/pdbsum/2z55 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=2z55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z55 RCSB], [http://www.ebi.ac.uk/pdbsum/2z55 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Archaea]]		[[Category: Archaea]]
-	[[Category: Kouyama, T.]]	+	[[Category: Kouyama, T]]
-	[[Category: Yoshimura, K.]]	+	[[Category: Yoshimura, K]]
	[[Category: Bacterioruberin]]		[[Category: Bacterioruberin]]
	[[Category: Retinal protein]]		[[Category: Retinal protein]]
	[[Category: Transport protein]]		[[Category: Transport protein]]

OCA at 06:58, 29 September 2014

OCA — Mon, 29 Sep 2014 06:58:05 GMT

←Older revision		Revision as of 06:58, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2z55.~~png~~\|~~left~~\|200px]]	+	==Bacterioruberin in the trimeric structure of archaerhodopsin-2==
		+	<StructureSection load='2z55' size='340' side='right' caption='[[2z55]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2z55]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaea Archaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z55 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=22B:BACTERIORUBERIN'>22B</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ei4\|2ei4]], [[1vgo\|1vgo]], [[1uaz\|1uaz]], [[1iw6\|1iw6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z55 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z55 RCSB], [http://www.ebi.ac.uk/pdbsum/2z55 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z5/2z55_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Archaerhodopsin-2 (aR2), a retinal protein-carotenoid complex found in the claret membrane of Halorubrum sp. aus-2, functions as a light-driven proton pump. In this study, the membrane fusion method was utilized to prepare trigonal P321 crystals (a=b=98.2 A, c=56.2 A) and hexagonal P6(3) crystals (a=b=108.8 A, c=220.7 A). The trigonal crystal is made up of stacked membranes in which the aR2 trimers are arranged on a honeycomb lattice. Similar membranous structures are found in the hexagonal crystal, but four membrane layers with different orientations are contained in the unit cell. In these crystals, the carotenoid bacterioruberin [5,32-bis(2-hydroxypropan-2-yl)-2,8,12,16,21,25,29,35-octamethylhexatriaco nta-6,8,10,12,14,16,18,20,22,24,26,28,30-tridecaene-2,35-diol] binds to crevices between the subunits of the trimer. Its polyene chain is inclined from the membrane normal by an angle of about 20 degrees and, on the cytoplasmic side, it is surrounded by helices AB and DE of neighbouring subunits. This peculiar binding mode suggests that bacterioruberin plays a striking structural role for the trimerization of aR2. When compared with the aR2 structure in another crystal form containing no bacterioruberin, the proton release channel takes a more closed conformation in the P321 or P6(3) crystal; i.e., the native conformation of protein is stabilized in the trimeric protein-bacterioruberin complex. Interestingly, most residues participating in the trimerization are not conserved in bacteriorhodopsin, a homologous protein capable of forming a trimeric structure in the absence of bacterioruberin. Despite a large alteration in the amino acid sequence, the shape of the intratrimer hydrophobic space filled by lipids is highly conserved between aR2 and bacteriorhodopsin. Since a transmembrane helix facing this space undergoes a large conformational change during the proton pumping cycle, it is feasible that trimerization is an important strategy to capture special lipid components that are relevant to the protein activity.

-	~~{{STRUCTURE_2z55\| PDB=2z55 \| SCENE= }}~~	+	Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2.,Yoshimura K, Kouyama T J Mol Biol. 2008 Feb 1;375(5):1267-81. Epub 2007 Nov 22. PMID:18082767<ref>PMID:18082767</ref>

-	~~===Bacterioruberin in~~ the ~~trimeric structure of archaerhodopsin-2===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18082767}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2z55]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Archaea Archaea]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA].~~	+

	==See Also==		==See Also==
	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]		*[[Bacteriorhodopsin\|Bacteriorhodopsin]]
	*[[Rhodopsin\|Rhodopsin]]		*[[Rhodopsin\|Rhodopsin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018082767<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Archaea]]		[[Category: Archaea]]
	[[Category: Kouyama, T.]]		[[Category: Kouyama, T.]]

OCA at 16:10, 20 October 2012

OCA — Sat, 20 Oct 2012 16:10:04 GMT

←Older revision		Revision as of 16:10, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2z55]] is a 4 chain structure ~~of [[Bacteriorhodopsin]] and [[Rhodopsin]]~~ with sequence from [http://en.wikipedia.org/wiki/Archaea Archaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA].	+	[[2z55]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaea Archaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA].

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

OCA: Protected "2z55" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 20:49:01 GMT

Protected "2z55" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:49, 26 July 2012

OCA at 20:49, 26 July 2012

OCA — Thu, 26 Jul 2012 20:49:00 GMT

←Older revision		Revision as of 20:49, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2z55.png\|left\|200px]]		[[Image:2z55.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2z55", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2z55\| PDB=2z55 \| SCENE= }}		{{STRUCTURE_2z55\| PDB=2z55 \| SCENE= }}

	===Bacterioruberin in the trimeric structure of archaerhodopsin-2===		===Bacterioruberin in the trimeric structure of archaerhodopsin-2===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18082767}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18082767 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18082767}}		{{ABSTRACT_PUBMED_18082767}}

	==About this Structure==		==About this Structure==
-	~~2Z55~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/~~Halobacterium_sp. Halobacterium sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA].	+	[[2z55]] is a 4 chain structure of [[Bacteriorhodopsin]] and [[Rhodopsin]] with sequence from [http://en.wikipedia.org/wiki/Archaea Archaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA].
		+
		+	==See Also==
		+	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]
		+	*[[Rhodopsin\|Rhodopsin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18082767~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018082767</ref><references group="xtra"/>
-	[[Category: ~~Halobacterium sp.~~]]	+	[[Category: Archaea]]
	[[Category: Kouyama, T.]]		[[Category: Kouyama, T.]]
	[[Category: Yoshimura, K.]]		[[Category: Yoshimura, K.]]
Line 30:		Line 22:
	[[Category: Retinal protein]]		[[Category: Retinal protein]]
	[[Category: Transport protein]]		[[Category: Transport protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:03:06 2009''

OCA at 13:03, 17 February 2009

OCA — Tue, 17 Feb 2009 13:03:06 GMT

←Older revision		Revision as of 13:03, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2Z55 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Halobacterium_sp. Halobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA].	+	2Z55 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Halobacterium_sp. Halobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z55 OCA].

	==Reference==		==Reference==
-	~~Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2., Yoshimura K, Kouyama T, J Mol Biol. 2008 Feb 1;375(5):1267-81. Epub 2007 Nov 22.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18082767 18082767]~~	+	<ref group="xtra">PMID:18082767</ref><references group="xtra"/>
	[[Category: Halobacterium sp.]]		[[Category: Halobacterium sp.]]
-	[[Category: Single protein]]
	[[Category: Kouyama, T.]]		[[Category: Kouyama, T.]]
	[[Category: Yoshimura, K.]]		[[Category: Yoshimura, K.]]
Line 32:		Line 31:
	[[Category: Transport protein]]		[[Category: Transport protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 20~~:37:~~42 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:03:06 2009''