5ztl - Revision history

OCA at 09:06, 22 November 2023

OCA — Wed, 22 Nov 2023 09:06:52 GMT

←Older revision		Revision as of 09:06, 22 November 2023
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	==Non-cryogenic structure of light-driven chloride pump having an NTQ motif==		==Non-cryogenic structure of light-driven chloride pump having an NTQ motif==
-	<StructureSection load='5ztl' size='340' side='right' caption='[[5ztl]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5ztl' size='340' side='right'caption='[[5ztl]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ztl]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"nonlabens_marina"_park_et_al._2012 "nonlabens marina" park et al. 2012~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZTL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZTL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ztl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nonlabens_marinus Nonlabens marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZTL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZTL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</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]] 1.85Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ClR, NMS_1267 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=930802 "Nonlabens marina" Park et al. 2012])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</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=5ztl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ztl OCA], [~~http~~://pdbe.org/5ztl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ztl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ztl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ztl 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=5ztl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ztl OCA], [https://pdbe.org/5ztl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ztl RCSB], [https://www.ebi.ac.uk/pdbsum/5ztl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ztl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/W8VZW3_9FLAO W8VZW3_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 5ztl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ztl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Rhodopsin 3D structures\|Rhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Nonlabens marina park et al. 2012~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Lee, W~~]]	+	[[Category: Nonlabens marinus]]
-	[[Category: ~~Liu, H~~]]	+	[[Category: Lee W]]
-	[[Category: ~~Park, S Y]]~~	+	[[Category: Liu H]]
-	~~[[Category: Yun, J~~ H]]	+	[[Category: Park SY]]
-	[[Category: ~~Chloride pump~~]]	+	[[Category: Yun JH]]
-	[[Category: ~~Serial femtosecond crystallography]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: X-ray free electron laser~~]]	+

OCA at 06:17, 2 January 2019

OCA — Wed, 02 Jan 2019 06:17:54 GMT

←Older revision		Revision as of 06:17, 2 January 2019
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	<StructureSection load='5ztl' size='340' side='right' caption='[[5ztl]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5ztl' size='340' side='right' caption='[[5ztl]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ztl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZTL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZTL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ztl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"nonlabens_marina"_park_et_al._2012 "nonlabens marina" park et al. 2012]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZTL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZTL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ClR, NMS_1267 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=930802 "Nonlabens marina" Park et al. 2012])</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=5ztl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ztl OCA], [http://pdbe.org/5ztl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ztl RCSB], [http://www.ebi.ac.uk/pdbsum/5ztl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ztl 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=5ztl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ztl OCA], [http://pdbe.org/5ztl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ztl RCSB], [http://www.ebi.ac.uk/pdbsum/5ztl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ztl ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Nonlabens marina park et al. 2012]]
	[[Category: Lee, W]]		[[Category: Lee, W]]
	[[Category: Liu, H]]		[[Category: Liu, H]]

OCA at 06:31, 5 December 2018

OCA — Wed, 05 Dec 2018 06:31:05 GMT

←Older revision		Revision as of 06:31, 5 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ztl is ~~ON HOLD until Paper~~ Publication	+	==Non-cryogenic structure of light-driven chloride pump having an NTQ motif==
		+	<StructureSection load='5ztl' size='340' side='right' caption='[[5ztl]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ztl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZTL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZTL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</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=5ztl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ztl OCA], [http://pdbe.org/5ztl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ztl RCSB], [http://www.ebi.ac.uk/pdbsum/5ztl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ztl ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate due to a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 A, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all-trans retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main- and sidechains as well as of chloride and water molecules due to temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.

-	~~Authors~~:	+	Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency.,Yun JH, Li X, Park JH, Wang Y, Ohki M, Jin Z, Lee W, Park SY, Hu H, Li C, Zatsepin N, Hunter MS, Sierra RG, Koralek J, Yoon CH, Cho HS, Weierstall U, Tang L, Liu H, Lee W J Biol Chem. 2018 Nov 19. pii: RA118.004038. doi: 10.1074/jbc.RA118.004038. PMID:30455349<ref>PMID:30455349</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ztl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lee, W]]
		+	[[Category: Liu, H]]
		+	[[Category: Park, S Y]]
		+	[[Category: Yun, J H]]
		+	[[Category: Chloride pump]]
		+	[[Category: Serial femtosecond crystallography]]
		+	[[Category: Transport protein]]
		+	[[Category: X-ray free electron laser]]

OCA at 06:05, 10 October 2018

OCA — Wed, 10 Oct 2018 06:05:22 GMT

←Older revision		Revision as of 06:05, 10 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ztl is ON HOLD	+	The entry 5ztl is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 09 May 2018 04:47:08 GMT

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

←Older revision

Revision as of 04:47, 9 May 2018

OCA: New page: '''Unreleased structure''' The entry 5ztl is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 09 May 2018 04:47:07 GMT

New page: '''Unreleased structure''' The entry 5ztl is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ztl is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]