5mad - Revision history

OCA at 18:34, 1 November 2023

OCA — Wed, 01 Nov 2023 18:34:57 GMT

←Older revision		Revision as of 18:34, 1 November 2023
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	<StructureSection load='5mad' size='340' side='right'caption='[[5mad]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='5mad' size='340' side='right'caption='[[5mad]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mad]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MAD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5MAD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mad]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MAD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~, ~~<scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.53Å</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='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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5mad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mad OCA], [~~http~~://pdbe.org/5mad PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mad RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mad PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mad 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=5mad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mad OCA], [https://pdbe.org/5mad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mad RCSB], [https://www.ebi.ac.uk/pdbsum/5mad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mad ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aequorea victoria]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Batyuk, A]]	+	[[Category: Synthetic construct]]
-	[[Category: Bojar, D]]	+	[[Category: Batyuk A]]
-	[[Category: Ernst, P]]	+	[[Category: Bojar D]]
-	[[Category: Hansen, S]]	+	[[Category: Ernst P]]
-	[[Category: Koch, A]]	+	[[Category: Hansen S]]
-	[[Category: Plueckthun, A]]	+	[[Category: Koch A]]
-	[[Category: Stueber, J]]	+	[[Category: Plueckthun A]]
-	~~[[Category: Designed ankyrin protein]]~~	+	[[Category: Stueber J]]
-	~~[[Category: Fluorescent protein]]~~	+
-	~~[[Category: Green fluorescent protein~~]]	+

OCA at 07:13, 19 August 2020

OCA — Wed, 19 Aug 2020 07:13:48 GMT

←Older revision		Revision as of 07:13, 19 August 2020
Line 1:		Line 1:

	==GFP-binding DARPin 3G61==		==GFP-binding DARPin 3G61==
-	<StructureSection load='5mad' size='340' side='right' caption='[[5mad]], [[Resolution\|resolution]] 1.53Å' scene=''>	+	<StructureSection load='5mad' size='340' side='right'caption='[[5mad]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mad]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MAD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MAD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mad]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MAD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MAD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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='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='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=5mad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mad OCA], [http://pdbe.org/5mad PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mad RCSB], [http://www.ebi.ac.uk/pdbsum/5mad PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mad 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=5mad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mad OCA], [http://pdbe.org/5mad PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mad RCSB], [http://www.ebi.ac.uk/pdbsum/5mad PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mad ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5mad" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5mad" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Green Fluorescent Protein 3D structures\|Green Fluorescent Protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Batyuk, A]]		[[Category: Batyuk, A]]
	[[Category: Bojar, D]]		[[Category: Bojar, D]]

OCA at 07:09, 6 December 2017

OCA — Wed, 06 Dec 2017 07:09:33 GMT

←Older revision		Revision as of 07:09, 6 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5mad is ~~ON HOLD until Paper~~ Publication	+	==GFP-binding DARPin 3G61==
		+	<StructureSection load='5mad' size='340' side='right' caption='[[5mad]], [[Resolution\|resolution]] 1.53Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5mad]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MAD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MAD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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='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=5mad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mad OCA], [http://pdbe.org/5mad PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mad RCSB], [http://www.ebi.ac.uk/pdbsum/5mad PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mad ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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 ==
		+	Green fluorescent protein (GFP) fusions are pervasively used to study structures and processes. Specific GFP-binders are thus of great utility for detection, immobilization or manipulation of GFP-fused molecules. We determined structures of two designed ankyrin repeat proteins (DARPins), complexed with GFP, which revealed different but overlapping epitopes. Here we show a structure-guided design strategy that, by truncation and computational reengineering, led to a stable construct where both can bind simultaneously: by linkage of the two binders, fusion constructs were obtained that "wrap around" GFP, have very high affinities of about 10-30 pM, and extremely slow off-rates. They can be natively produced in E. coli in very large amounts, and show excellent biophysical properties. Their very high stability and affinity, facile site-directed functionalization at introduced unique lysines or cysteines facilitate many applications. As examples, we present them as tight yet reversible immobilization reagents for surface plasmon resonance, as fluorescently labelled monomeric detection reagents in flow cytometry, as pull-down ligands to selectively enrich GFP fusion proteins from cell extracts, and as affinity column ligands for inexpensive large-scale protein purification. We have thus described a general design strategy to create a "clamp" from two different high-affinity repeat proteins, even if their epitopes overlap.

-	~~Authors: Hansen~~, S., ~~Stueber, J.~~, Ernst, P., Koch, A., Bojar, D., Batyuk, A~~., Plueckthun~~, A.	+	Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity.,Hansen S, Stuber JC, Ernst P, Koch A, Bojar D, Batyuk A, Pluckthun A Sci Rep. 2017 Nov 24;7(1):16292. doi: 10.1038/s41598-017-15711-z. PMID:29176615<ref>PMID:29176615</ref>

-	~~Description: GFP-binding DARPin 3G61~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Stueber, J]]~~	+	<div class="pdbe-citations 5mad" style="background-color:#fffaf0;"></div>
-	~~[[Category: Plueckthun, A]]~~	+	== References ==
-	~~[[Category: Koch, A]]~~	+	<references/>
-	~~[[Category: Ernst, P]]~~	+	__TOC__
-	~~[[Category: Bojar, D]]~~	+	</StructureSection>
	[[Category: Batyuk, A]]		[[Category: Batyuk, A]]
		+	[[Category: Bojar, D]]
		+	[[Category: Ernst, P]]
	[[Category: Hansen, S]]		[[Category: Hansen, S]]
		+	[[Category: Koch, A]]
		+	[[Category: Plueckthun, A]]
		+	[[Category: Stueber, J]]
		+	[[Category: Designed ankyrin protein]]
		+	[[Category: Fluorescent protein]]
		+	[[Category: Green fluorescent protein]]

OCA at 11:09, 9 March 2017

OCA — Thu, 09 Mar 2017 11:09:33 GMT

←Older revision		Revision as of 11:09, 9 March 2017
Line 7:		Line 7:
	Description: GFP-binding DARPin 3G61		Description: GFP-binding DARPin 3G61
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Koch, A]]
-	[[Category: Bojar, D]]
-	[[Category: Hansen, S]]
	[[Category: Stueber, J]]		[[Category: Stueber, J]]
	[[Category: Plueckthun, A]]		[[Category: Plueckthun, A]]
		+	[[Category: Koch, A]]
	[[Category: Ernst, P]]		[[Category: Ernst, P]]
		+	[[Category: Bojar, D]]
	[[Category: Batyuk, A]]		[[Category: Batyuk, A]]
		+	[[Category: Hansen, S]]

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

OCA — Fri, 09 Dec 2016 16:33:57 GMT

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

←Older revision

Revision as of 16:33, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5mad is ON HOLD until Paper Publication Authors: Hansen, S., Stueber, J., Ernst, P., Koch, A., Bojar, D., Batyuk, A., Plueckthun, A. Description: G...

OCA — Fri, 09 Dec 2016 16:33:56 GMT

New page: '''Unreleased structure''' The entry 5mad is ON HOLD until Paper Publication Authors: Hansen, S., Stueber, J., Ernst, P., Koch, A., Bojar, D., Batyuk, A., Plueckthun, A. Description: G...

New page

'''Unreleased structure'''

The entry 5mad is ON HOLD until Paper Publication

Authors: Hansen, S., Stueber, J., Ernst, P., Koch, A., Bojar, D., Batyuk, A., Plueckthun, A.

Description: GFP-binding DARPin 3G61
[[Category: Unreleased Structures]]
[[Category: Koch, A]]
[[Category: Bojar, D]]
[[Category: Hansen, S]]
[[Category: Stueber, J]]
[[Category: Plueckthun, A]]
[[Category: Ernst, P]]
[[Category: Batyuk, A]]