5y8r - Revision history

OCA at 08:24, 22 November 2023

OCA — Wed, 22 Nov 2023 08:24:39 GMT

←Older revision		Revision as of 08:24, 22 November 2023
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	<StructureSection load='5y8r' size='340' side='right'caption='[[5y8r]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5y8r' size='340' side='right'caption='[[5y8r]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y8r]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Green_polyp Green polyp~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y8R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Y8R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y8r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zoanthus_sp. Zoanthus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y8R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y8R FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH7:[(4Z)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-2-(3,4,5,6-TETRAHYDROPYRIDIN-2-YL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CH7</scene>, <scene name='pdbligand=NFA:PHENYLALANINE+AMIDE'>NFA</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5y8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8r OCA], [~~http~~://pdbe.org/5y8r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y8r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y8r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8r ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CH7:[(4Z)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-2-(3,4,5,6-TETRAHYDROPYRIDIN-2-YL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CH7</scene>, <scene name='pdbligand=NFA:PHENYLALANINE+AMIDE'>NFA</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=5y8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8r OCA], [https://pdbe.org/5y8r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y8r RCSB], [https://www.ebi.ac.uk/pdbsum/5y8r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GFPL2_ZOASP GFPL2_ZOASP]] Pigment protein that is yellow in color.<ref>PMID:10504696</ref> <ref>PMID:15628861</ref>	+	[https://www.uniprot.org/uniprot/GFPL2_ZOASP GFPL2_ZOASP] Pigment protein that is yellow in color.<ref>PMID:10504696</ref> <ref>PMID:15628861</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: Green polyp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bae, J E~~]]	+	[[Category: Zoanthus sp]]
-	[[Category: ~~Kim, I J~~]]	+	[[Category: Bae JE]]
-	[[Category: ~~Nam, K H~~]]	+	[[Category: Kim IJ]]
-	[[Category: ~~Fluorescent protein]]~~	+	[[Category: Nam KH]]
-	~~[[Category: Ph]]~~	+
-	~~[[Category: Zsyellow~~]]	+

OCA at 09:13, 21 October 2020

OCA — Wed, 21 Oct 2020 09:13:14 GMT

←Older revision		Revision as of 09:13, 21 October 2020
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	==ZsYellow at pH 3.5==		==ZsYellow at pH 3.5==
-	<StructureSection load='5y8r' size='340' side='right' caption='[[5y8r]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5y8r' size='340' side='right'caption='[[5y8r]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y8r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Green_polyp Green polyp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y8R OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y8R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y8r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Green_polyp Green polyp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y8R OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Y8R FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH7:[(4Z)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-2-(3,4,5,6-TETRAHYDROPYRIDIN-2-YL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CH7</scene>, <scene name='pdbligand=NFA:PHENYLALANINE+AMIDE'>NFA</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH7:[(4Z)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-2-(3,4,5,6-TETRAHYDROPYRIDIN-2-YL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CH7</scene>, <scene name='pdbligand=NFA:PHENYLALANINE+AMIDE'>NFA</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=5y8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8r OCA], [http://pdbe.org/5y8r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y8r RCSB], [http://www.ebi.ac.uk/pdbsum/5y8r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8r 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=5y8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8r OCA], [http://pdbe.org/5y8r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y8r RCSB], [http://www.ebi.ac.uk/pdbsum/5y8r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Green polyp]]		[[Category: Green polyp]]
		+	[[Category: Large Structures]]
	[[Category: Bae, J E]]		[[Category: Bae, J E]]
	[[Category: Kim, I J]]		[[Category: Kim, I J]]

OCA at 20:49, 2 December 2018

OCA — Sun, 02 Dec 2018 20:49:13 GMT

←Older revision		Revision as of 20:49, 2 December 2018
Line 3:		Line 3:
	<StructureSection load='5y8r' size='340' side='right' caption='[[5y8r]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5y8r' size='340' side='right' caption='[[5y8r]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y8r]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y8R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y8R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y8r]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Green_polyp Green polyp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y8R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y8R FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH7:[(4Z)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-2-(3,4,5,6-TETRAHYDROPYRIDIN-2-YL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CH7</scene>, <scene name='pdbligand=NFA:PHENYLALANINE+AMIDE'>NFA</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH7:[(4Z)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-2-(3,4,5,6-TETRAHYDROPYRIDIN-2-YL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CH7</scene>, <scene name='pdbligand=NFA:PHENYLALANINE+AMIDE'>NFA</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=5y8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8r OCA], [http://pdbe.org/5y8r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y8r RCSB], [http://www.ebi.ac.uk/pdbsum/5y8r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8r 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=5y8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8r OCA], [http://pdbe.org/5y8r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y8r RCSB], [http://www.ebi.ac.uk/pdbsum/5y8r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8r ProSAT]</span></td></tr>
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GFPL2_ZOASP GFPL2_ZOASP]] Pigment protein that is yellow in color.<ref>PMID:10504696</ref> <ref>PMID:15628861</ref>		[[http://www.uniprot.org/uniprot/GFPL2_ZOASP GFPL2_ZOASP]] Pigment protein that is yellow in color.<ref>PMID:10504696</ref> <ref>PMID:15628861</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many fluorescent proteins (FPs) exhibit fluorescence quenching at a low pH. This pH-induced non-fluorescent state of an FP serves as a useful indicator of the cellular pH. ZsYellow is widely used as an optical marker in molecular biology, but its pH-induced non-fluorescent state has not been characterized. Here, we report the pH-dependent spectral properties of ZsYellow, which exhibited the pH-induced non-fluorescence state at a pH below 4.0. We determined the crystal structures of ZsYellow at pH 3.5 (non-fluorescence state) and 8.0 (fluorescence state), which revealed the cis-configuration of the chromophore without pH-induced isomerization. In the non-fluorescence state, Arg95, which is involved in stabilization of the exited state of the chromophore, was found to more loosely interact with the carbonyl oxygen atom of the chromophore when compared to the interaction at pH 8.0. In the fluorescence state, Glu221, which is involved in the hydrogen bonding network around the chromophore, stably interacted with Gln42 and His202. By contrast, in the non-fluorescence state, the protonated conserved Glu221 residue exhibited a large conformational change and was separated from His202 by 5.46 A, resulting in breakdown of the hydrogen bond network. Our results provide insight into the critical role of the conserved Glu221 residue for generating the pH-induced non-fluorescent state.
		+
		+	Disruption of the hydrogen bonding network determines the pH-induced non-fluorescent state of the fluorescent protein ZsYellow by protonation of Glu221.,Bae JE, Kim IJ, Nam KH Biochem Biophys Res Commun. 2017 Nov 4;493(1):562-567. doi:, 10.1016/j.bbrc.2017.08.152. Epub 2017 Sep 1. PMID:28867188<ref>PMID:28867188</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5y8r" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Green polyp]]
	[[Category: Bae, J E]]		[[Category: Bae, J E]]
	[[Category: Kim, I J]]		[[Category: Kim, I J]]

OCA: Protected "5y8r" [edit=sysop:move=sysop]

OCA — Fri, 06 Oct 2017 05:37:12 GMT

Protected "5y8r" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:37, 6 October 2017

OCA: New page: ==ZsYellow at pH 3.5== == Structural highlights ==
OCA — Fri, 06 Oct 2017 05:37:10 GMT

New page: ==ZsYellow at pH 3.5== <StructureSection load='5y8r' size='340' side='right' caption='5y8r, resolution 2.30Å' scene=''> == Structural highlights == <table><tr><td...

New page

==ZsYellow at pH 3.5==
<StructureSection load='5y8r' size='340' side='right' caption='[[5y8r]], [[Resolution|resolution]] 2.30Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5y8r]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y8R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y8R FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH7:[(4Z)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-2-(3,4,5,6-TETRAHYDROPYRIDIN-2-YL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CH7</scene>, <scene name='pdbligand=NFA:PHENYLALANINE+AMIDE'>NFA</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=5y8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y8r OCA], [http://pdbe.org/5y8r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y8r RCSB], [http://www.ebi.ac.uk/pdbsum/5y8r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y8r ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/GFPL2_ZOASP GFPL2_ZOASP]] Pigment protein that is yellow in color.<ref>PMID:10504696</ref> <ref>PMID:15628861</ref>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Bae, J E]]
[[Category: Kim, I J]]
[[Category: Nam, K H]]
[[Category: Fluorescent protein]]
[[Category: Ph]]
[[Category: Zsyellow]]