5g36 - Revision history

OCA at 13:37, 26 July 2023

OCA — Wed, 26 Jul 2023 13:37:11 GMT

←Older revision		Revision as of 13:37, 26 July 2023
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	<StructureSection load='5g36' size='340' side='right'caption='[[5g36]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5g36' size='340' side='right'caption='[[5g36]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5g36]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_halobius_ruber"_klebahn_1919 "bacillus halobius ruber" klebahn 1919~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G36 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5G36 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5g36]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G36 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5G36 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=CL:CHLORIDE+ION'>CL</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]] 2.6Å</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=5g36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g36 OCA], [~~http~~://pdbe.org/5g36 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5g36 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5g36 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5g36 ProSAT]</span></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=CL:CHLORIDE+ION'>CL</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=5g36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g36 OCA], [https://pdbe.org/5g36 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5g36 RCSB], [https://www.ebi.ac.uk/pdbsum/5g36 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5g36 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BACH_HALS3 BACH_HALS3]] Light-driven chloride pump.<ref>PMID:24409552</ref>	+	[https://www.uniprot.org/uniprot/BACH_HALS3 BACH_HALS3] Light-driven chloride pump.<ref>PMID:24409552</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus halobius ruber klebahn 1919~~]]	+	[[Category: Halobacterium salinarum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Heberle, J]]	+	[[Category: Heberle J]]
-	[[Category: Niemann~~, H H~~]]	+	[[Category: Niemann HH]]
-	[[Category: Schlesinger, R]]	+	[[Category: Schlesinger R]]
-	[[Category: Schreiner, M]]	+	[[Category: Schreiner M]]
-	~~[[Category: Archaeal rhodopsin]]~~	+
-	~~[[Category: Halophilic archaea]]~~	+
-	~~[[Category: Ion transmembrane transport]]~~	+
-	~~[[Category: Light driven ion pump]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Retinal protein]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 13:02, 10 May 2019

OCA — Fri, 10 May 2019 13:02:09 GMT

←Older revision		Revision as of 13:02, 10 May 2019
Line 1:		Line 1:

	==Yellow form of Halorhodopsin from Halobacterium salinarum in a new rhombohedral crystal form==		==Yellow form of Halorhodopsin from Halobacterium salinarum in a new rhombohedral crystal form==
-	<StructureSection load='5g36' size='340' side='right' caption='[[5g36]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5g36' size='340' side='right'caption='[[5g36]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5g36]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G36 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5G36 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5g36]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_halobius_ruber"_klebahn_1919 "bacillus halobius ruber" klebahn 1919]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G36 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5G36 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=CL:CHLORIDE+ION'>CL</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=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=5g36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g36 OCA], [http://pdbe.org/5g36 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g36 RCSB], [http://www.ebi.ac.uk/pdbsum/5g36 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g36 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=5g36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g36 OCA], [http://pdbe.org/5g36 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g36 RCSB], [http://www.ebi.ac.uk/pdbsum/5g36 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g36 ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 5g36" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5g36" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bacteriorhodopsin 3D structures\|Bacteriorhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus halobius ruber klebahn 1919]]
		+	[[Category: Large Structures]]
	[[Category: Heberle, J]]		[[Category: Heberle, J]]
	[[Category: Niemann, H H]]		[[Category: Niemann, H H]]

OCA at 13:53, 5 October 2016

OCA — Wed, 05 Oct 2016 13:53:17 GMT

←Older revision		Revision as of 13:53, 5 October 2016
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BACH_HALS3 BACH_HALS3]] Light-driven chloride pump.<ref>PMID:24409552</ref>		[[http://www.uniprot.org/uniprot/BACH_HALS3 BACH_HALS3]] Light-driven chloride pump.<ref>PMID:24409552</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The transmembrane pump halorhodopsin in halophilic archaea translocates chloride ions from the extracellular to the cytoplasmic side upon illumination. In the ground state a tightly bound chloride ion occupies the primary chloride-binding site (CBS I) close to the protonated Schiff base that links the retinal chromophore to the protein. The light-triggered trans-cis isomerization of retinal causes structural changes in the protein associated with movement of the chloride ion. In reverse, chemical depletion of CBS I in Natronomonas pharaonis halorhodopsin (NpHR) through deprotonation of the Schiff base results in conformational changes of the protein: a state thought to mimic late stages of the photocycle. Here, crystals of Halobacterium salinarum halorhodopsin (HsHR) were soaked at high pH to provoke deprotonation of the Schiff base and loss of chloride. The crystals changed colour from purple to yellow and the occupancy of CBS I was reduced from 1 to about 0.5. In contrast to NpHR, this chloride depletion did not cause substantial conformational changes in the protein. Nevertheless, two observations indicate that chloride depletion could eventually result in structural changes similar to those found in NpHR. Firstly, the partially chloride-depleted form of HsHR has increased normalized B factors in the region of helix C that is close to CBS I and changes its conformation in NpHR. Secondly, prolonged soaking of HsHR crystals at high pH resulted in loss of diffraction. In conclusion, the conformation of the chloride-free protein may not be compatible with this crystal form of HsHR despite a packing arrangement that hardly restrains helices E and F that presumably move during ion transport.
		+
		+	Crystal structure of Halobacterium salinarum halorhodopsin with a partially depopulated primary chloride-binding site.,Schreiner M, Schlesinger R, Heberle J, Niemann HH Acta Crystallogr F Struct Biol Commun. 2016 Sep;72(Pt 9):692-9. doi:, 10.1107/S2053230X16012796. Epub 2016 Aug 26. PMID:27599860<ref>PMID:27599860</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5g36" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:55, 10 September 2016

OCA — Sat, 10 Sep 2016 13:55:16 GMT

←Older revision		Revision as of 13:55, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5g36 ~~is ON HOLD~~	+	==Yellow form of Halorhodopsin from Halobacterium salinarum in a new rhombohedral crystal form==
-		+	<StructureSection load='5g36' size='340' side='right' caption='[[5g36]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~Authors~~: ~~Schreiner, M~~., ~~Schlesinger~~, R., ~~Heberle~~, J., ~~Niemann~~, H.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5g36]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G36 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5G36 FirstGlance]. <br>
-	~~Description~~: ~~Yellow form of Halorhodopsin from Halobacterium salinarum in a new rhombohedral crystal form~~	+	</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=CL:CHLORIDE+ION'>CL</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=5g36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g36 OCA], [http://pdbe.org/5g36 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g36 RCSB], [http://www.ebi.ac.uk/pdbsum/5g36 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g36 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BACH_HALS3 BACH_HALS3]] Light-driven chloride pump.<ref>PMID:24409552</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Heberle, J]]
		+	[[Category: Niemann, H H]]
	[[Category: Schlesinger, R]]		[[Category: Schlesinger, R]]
-	[[Category: Niemann, H.H]]
-	[[Category: Heberle, J]]
	[[Category: Schreiner, M]]		[[Category: Schreiner, M]]
		+	[[Category: Archaeal rhodopsin]]
		+	[[Category: Halophilic archaea]]
		+	[[Category: Ion transmembrane transport]]
		+	[[Category: Light driven ion pump]]
		+	[[Category: Membrane protein]]
		+	[[Category: Retinal protein]]
		+	[[Category: Transport protein]]

OCA: Protected "5g36" [edit=sysop:move=sysop]

OCA — Tue, 10 May 2016 23:27:02 GMT

Protected "5g36" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:27, 10 May 2016

OCA: New page: '''Unreleased structure''' The entry 5g36 is ON HOLD Authors: Schreiner, M., Schlesinger, R., Heberle, J., Niemann, H.H. Description: Yellow form of Halorhodopsin from Halobacterium sa...

OCA — Tue, 10 May 2016 23:27:01 GMT

New page: '''Unreleased structure''' The entry 5g36 is ON HOLD Authors: Schreiner, M., Schlesinger, R., Heberle, J., Niemann, H.H. Description: Yellow form of Halorhodopsin from Halobacterium sa...

New page

'''Unreleased structure'''

The entry 5g36 is ON HOLD

Authors: Schreiner, M., Schlesinger, R., Heberle, J., Niemann, H.H.

Description: Yellow form of Halorhodopsin from Halobacterium salinarum in a new rhombohedral crystal form
[[Category: Unreleased Structures]]
[[Category: Schlesinger, R]]
[[Category: Niemann, H.H]]
[[Category: Heberle, J]]
[[Category: Schreiner, M]]