7pd0 - Revision history

OCA at 13:04, 1 February 2024

2024-02-01T13:04:13Z

←Older revision		Revision as of 13:04, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7pd0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PD0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7pd0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PD0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=7pd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pd0 OCA], [https://pdbe.org/7pd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pd0 RCSB], [https://www.ebi.ac.uk/pdbsum/7pd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pd0 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=7pd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pd0 OCA], [https://pdbe.org/7pd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pd0 RCSB], [https://www.ebi.ac.uk/pdbsum/7pd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pd0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.	+	[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7pd0" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7pd0" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:25, 8 September 2022

2022-09-08T05:25:18Z

←Older revision		Revision as of 05:25, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7pd0' size='340' side='right'caption='[[7pd0]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='7pd0' size='340' side='right'caption='[[7pd0]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7pd0]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PD0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7pd0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PD0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat~~"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat~~"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene><~~/td~~></tr>	+
-	<~~tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"><div style~~=~~'overflow~~: ~~auto; max-height: 3em;~~'>~~[[7pca\|7pca]]~~</~~div~~></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=7pd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pd0 OCA], [https://pdbe.org/7pd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pd0 RCSB], [https://www.ebi.ac.uk/pdbsum/7pd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pd0 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=7pd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pd0 OCA], [https://pdbe.org/7pd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pd0 RCSB], [https://www.ebi.ac.uk/pdbsum/7pd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pd0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.	+	[[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aequorea victoria]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Becker, K]]	+	[[Category: Becker K]]
-	[[Category: Fritz-Wolf, K]]	+	[[Category: Fritz-Wolf K]]
-	[[Category: Heimsch~~, K C~~]]	+	[[Category: Heimsch KC]]
-	[[Category: Schuh~~, A K]]~~	+	[[Category: Schuh AK]]
-	~~[[Category: Dynamic simulation]]~~	+
-	~~[[Category: Fluorescent protein]]~~	+
-	~~[[Category: Genetically encoded biosensor]]~~	+
-	~~[[Category: Plasmodium falciparum]]~~	+
-	~~[[Category: Redox regulation]]~~	+
-	~~[[Category: X-ray crystal structure~~]]	+

OCA at 07:08, 20 July 2022

2022-07-20T07:08:11Z

←Older revision		Revision as of 07:08, 20 July 2022
Line 1:		Line 1:

	==Functional and structural characterization of redox sensitive superfolder green fluorescent protein and variants==		==Functional and structural characterization of redox sensitive superfolder green fluorescent protein and variants==
-	<StructureSection load='7pd0' size='340' side='right'caption='[[7pd0]]' scene=''>	+	<StructureSection load='7pd0' size='340' side='right'caption='[[7pd0]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PD0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7pd0]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PD0 FirstGlance]. <br>
-	</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=7pd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pd0 OCA], [https://pdbe.org/7pd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pd0 RCSB], [https://www.ebi.ac.uk/pdbsum/7pd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pd0 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7pca\|7pca]]</div></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=7pd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pd0 OCA], [https://pdbe.org/7pd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pd0 RCSB], [https://www.ebi.ac.uk/pdbsum/7pd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pd0 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/GFP_AEQVI GFP_AEQVI]] Energy-transfer acceptor. Its role is to transduce the blue chemiluminescence of the protein aequorin into green fluorescent light by energy transfer. Fluoresces in vivo upon receiving energy from the Ca(2+)-activated photoprotein aequorin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	AIMS: Genetically encoded GFP-based redox biosensors are widely used to monitor specific and dynamic redox processes in living cells. Over the last years, various biosensors for a variety of applications were engineered and enhanced to match the organism and cellular environments, which should be investigated. In this context, the unicellular intraerythrocytic parasite Plasmodium, the causative agent of malaria, represents a challenge, as the small size of the organism results in weak fluorescence signals that complicate precise measurements, especially for cell compartment-specific observations. To address this, we have functionally and structurally characterized an enhanced redox biosensor superfolder roGFP2 (sfroGFP2). RESULTS: SfroGFP2 retains roGFP2-like behavior, yet with improved fluorescence intensity in cellulo. SfroGFP2-based redox biosensors are pH-insensitive in a physiological pH range and show midpoint potentials comparable to roGFP2-based redox biosensors. Using crystallography and rigidity theory, we identified the superfolding mutations as being responsible for improved structural stability of the biosensor in a redox-sensitive environment, thus explaining the improved fluorescence intensity in cellulo. INNOVATION: This work provides insight into the structure and function of GFP-based redox biosensors. It describes an improved redox biosensor (sfroGFP2) suitable for measuring oxidizing effects within small cells where applicability of other redox sensor variants is limited. CONCLUSION: Improved structural stability of sfroGFP2 gives rise to increased fluorescence intensity in cellulo. Fusion to hGrx1 provides the hitherto most suitable biosensor for measuring oxidizing effects in Plasmodium. This sensor is of major interest for studying glutathione redox changes in small cells, as well as subcellular compartments in general.
		+
		+	Structure and function of redox-sensitive superfolder green fluorescent protein variant.,Heimsch K, Gertzen CW, Schuh K, Nietzel T, Rahlfs S, Przyborski J, Gohlke H, Schwarzlander M, Becker K, Fritz-Wolf K Antioxid Redox Signal. 2022 Jan 24. doi: 10.1089/ars.2021.0234. PMID:35072524<ref>PMID:35072524</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7pd0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Becker K]]	+	[[Category: Becker, K]]
-	[[Category: Fritz-Wolf K]]	+	[[Category: Fritz-Wolf, K]]
-	[[Category: Heimsch KC]]	+	[[Category: Heimsch, K C]]
-	[[Category: Schuh AK]]	+	[[Category: Schuh, A K]]
		+	[[Category: Dynamic simulation]]
		+	[[Category: Fluorescent protein]]
		+	[[Category: Genetically encoded biosensor]]
		+	[[Category: Plasmodium falciparum]]
		+	[[Category: Redox regulation]]
		+	[[Category: X-ray crystal structure]]

OCA at 10:16, 16 February 2022

2022-02-16T10:16:55Z

←Older revision		Revision as of 10:16, 16 February 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7pd0 ~~is ON HOLD until Paper Publication~~	+	==Functional and structural characterization of redox sensitive superfolder green fluorescent protein and variants==
-		+	<StructureSection load='7pd0' size='340' side='right'caption='[[7pd0]]' scene=''>
-	~~Authors~~: ~~Fritz~~-~~Wolf~~, K., ~~Heimsch~~, K.C., ~~Schuh, A~~.K., ~~Becker, K~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PD0 FirstGlance]. <br>
-	~~Description: Functional and structural characterization of redox sensitive superfolder green fluorescent protein and variants~~	+	</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=7pd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pd0 OCA], [https://pdbe.org/7pd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pd0 RCSB], [https://www.ebi.ac.uk/pdbsum/7pd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pd0 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Schuh, A.~~K]]	+	__TOC__
-	[[Category: ~~Becker,~~ K]]	+	</StructureSection>
-	[[Category: Heimsch~~, K.C~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Fritz-Wolf, K~~]]	+	[[Category: Becker K]]
		+	[[Category: Fritz-Wolf K]]
		+	[[Category: Heimsch KC]]
		+	[[Category: Schuh AK]]

OCA at 05:00, 18 August 2021

2021-08-18T05:00:38Z

←Older revision		Revision as of 05:00, 18 August 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7pd0 is ON HOLD until ~~sometime in the future~~	+	The entry 7pd0 is ON HOLD until Paper Publication

	Authors: Fritz-Wolf, K., Heimsch, K.C., Schuh, A.K., Becker, K.		Authors: Fritz-Wolf, K., Heimsch, K.C., Schuh, A.K., Becker, K.

OCA: Protected "7pd0" [edit=sysop:move=sysop]

2021-08-11T05:06:44Z

Protected "7pd0" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:06, 11 August 2021

OCA: New page: '''Unreleased structure''' The entry 7pd0 is ON HOLD until sometime in the future Authors: Fritz-Wolf, K., Heimsch, K.C., Schuh, A.K., Becker, K. Description: Functional and structural...

2021-08-11T05:06:43Z

New page: '''Unreleased structure''' The entry 7pd0 is ON HOLD until sometime in the future Authors: Fritz-Wolf, K., Heimsch, K.C., Schuh, A.K., Becker, K. Description: Functional and structural...

New page

'''Unreleased structure'''

The entry 7pd0 is ON HOLD until sometime in the future

Authors: Fritz-Wolf, K., Heimsch, K.C., Schuh, A.K., Becker, K.

Description: Functional and structural characterization of redox sensitive superfolder green fluorescent protein and variants
[[Category: Unreleased Structures]]
[[Category: Schuh, A.K]]
[[Category: Becker, K]]
[[Category: Heimsch, K.C]]
[[Category: Fritz-Wolf, K]]