5aao - Revision history

OCA at 11:06, 10 January 2024

2024-01-10T11:06:39Z

←Older revision		Revision as of 11:06, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5aao]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AAO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AAO FirstGlance]. <br>		<table><tr><td colspan='2'>[[5aao]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AAO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AAO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6FE:4-[[4-(DIMETHYLAMINO)CYCLOHEXA-2,5-DIEN-1-YLIDENE]-(4-METHOXYPHENYL)METHYL]-N,N-DIMETHYL-ANILINE'>6FE</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6FE:4-[[4-(DIMETHYLAMINO)CYCLOHEXA-2,5-DIEN-1-YLIDENE]-(4-METHOXYPHENYL)METHYL]-N,N-DIMETHYL-ANILINE'>6FE</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=5aao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aao OCA], [https://pdbe.org/5aao PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5aao RCSB], [https://www.ebi.ac.uk/pdbsum/5aao PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5aao 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=5aao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aao OCA], [https://pdbe.org/5aao PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5aao RCSB], [https://www.ebi.ac.uk/pdbsum/5aao PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5aao ProSAT]</span></td></tr>
	</table>		</table>

OCA at 04:48, 25 May 2023

2023-05-25T04:48:05Z

←Older revision		Revision as of 04:48, 25 May 2023
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	<StructureSection load='5aao' size='340' side='right'caption='[[5aao]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5aao' size='340' side='right'caption='[[5aao]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5aao]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AAO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AAO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5aao]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AAO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AAO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FE:4-[[4-(DIMETHYLAMINO)CYCLOHEXA-2,5-DIEN-1-YLIDENE]-(4-METHOXYPHENYL)METHYL]-N,N-DIMETHYL-ANILINE'>6FE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6FE:4-[[4-(DIMETHYLAMINO)CYCLOHEXA-2,5-DIEN-1-YLIDENE]-(4-METHOXYPHENYL)METHYL]-N,N-DIMETHYL-ANILINE'>6FE</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=5aao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aao OCA], [~~http~~://pdbe.org/5aao PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5aao RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5aao PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5aao 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=5aao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aao OCA], [https://pdbe.org/5aao PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5aao RCSB], [https://www.ebi.ac.uk/pdbsum/5aao PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5aao ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Batyuk, A]]	+	[[Category: Batyuk A]]
-	[[Category: Kummer, L]]	+	[[Category: Kummer L]]
-	[[Category: Mittl, P]]	+	[[Category: Mittl P]]
-	[[Category: Plueckthun, A]]	+	[[Category: Plueckthun A]]
-	[[Category: Schuetz, M]]	+	[[Category: Schuetz M]]
-	[[Category: Wu, Y]]	+	[[Category: Wu Y]]
-	~~[[Category: Fluorescent protein]]~~	+
-	~~[[Category: Fluorogen-activation]]~~	+
-	~~[[Category: Homodimer]]~~	+
-	~~[[Category: Malachite green~~]]	+

OCA at 08:38, 26 June 2019

2019-06-26T08:38:39Z

←Older revision		Revision as of 08:38, 26 June 2019
Line 1:		Line 1:

	==Crystal structure of fluorogen-activating designed ankyrin repeat protein (DARPin) dimer in complex with malachite green==		==Crystal structure of fluorogen-activating designed ankyrin repeat protein (DARPin) dimer in complex with malachite green==
-	<StructureSection load='5aao' size='340' side='right' caption='[[5aao]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5aao' size='340' side='right'caption='[[5aao]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5aao]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AAO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AAO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5aao]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AAO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AAO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FE:4-[[4-(DIMETHYLAMINO)CYCLOHEXA-2,5-DIEN-1-YLIDENE]-(4-METHOXYPHENYL)METHYL]-N,N-DIMETHYL-ANILINE'>6FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FE:4-[[4-(DIMETHYLAMINO)CYCLOHEXA-2,5-DIEN-1-YLIDENE]-(4-METHOXYPHENYL)METHYL]-N,N-DIMETHYL-ANILINE'>6FE</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=5aao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aao OCA], [http://pdbe.org/5aao PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5aao RCSB], [http://www.ebi.ac.uk/pdbsum/5aao PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5aao 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=5aao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aao OCA], [http://pdbe.org/5aao PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5aao RCSB], [http://www.ebi.ac.uk/pdbsum/5aao PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5aao ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct sequences]]
	[[Category: Batyuk, A]]		[[Category: Batyuk, A]]
	[[Category: Kummer, L]]		[[Category: Kummer, L]]

OCA at 09:54, 22 March 2017

2017-03-22T09:54:57Z

←Older revision		Revision as of 09:54, 22 March 2017
Line 1:		Line 1:
		+
	==Crystal structure of fluorogen-activating designed ankyrin repeat protein (DARPin) dimer in complex with malachite green==		==Crystal structure of fluorogen-activating designed ankyrin repeat protein (DARPin) dimer in complex with malachite green==
	<StructureSection load='5aao' size='340' side='right' caption='[[5aao]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5aao' size='340' side='right' caption='[[5aao]], [[Resolution\|resolution]] 2.60Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[5aao]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AAO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AAO FirstGlance]. <br>		<table><tr><td colspan='2'>[[5aao]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AAO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AAO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FE:4-[[4-(DIMETHYLAMINO)CYCLOHEXA-2,5-DIEN-1-YLIDENE]-(4-METHOXYPHENYL)METHYL]-N,N-DIMETHYL-ANILINE'>6FE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FE:4-[[4-(DIMETHYLAMINO)CYCLOHEXA-2,5-DIEN-1-YLIDENE]-(4-METHOXYPHENYL)METHYL]-N,N-DIMETHYL-ANILINE'>6FE</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=5aao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aao OCA], [http://pdbe.org/5aao PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5aao RCSB], [http://www.ebi.ac.uk/pdbsum/5aao PDBsum]</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=5aao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aao OCA], [http://pdbe.org/5aao PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5aao RCSB], [http://www.ebi.ac.uk/pdbsum/5aao PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5aao ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Fluorescent probes constitute a valuable toolbox to address a variety of biological questions and they have become irreplaceable for imaging methods. Commonly, such probes consist of fluorescent proteins or small organic fluorophores coupled to biological molecules of interest. Recently, a novel class of fluorescence-based probes, fluorogen-activating proteins (FAPs), has been reported. These binding proteins are based on antibody single-chain variable fragments and activate fluorogenic dyes, which only become fluorescent upon activation and do not fluoresce when free in solution. Here we present a novel class of fluorogen activators, termed FADAs, based on the very robust designed ankyrin repeat protein scaffold, which also readily folds in the reducing environment of the cytoplasm. The FADA generated in this study was obtained by combined selections with ribosome display and yeast surface display. It enhances the fluorescence of malachite green (MG) dyes by a factor of more than 11,000 and thus activates MG to a similar extent as FAPs based on single-chain variable fragments. As shown by structure determination and in vitro measurements, this FADA was evolved to form a homodimer for the activation of MG dyes. Exploiting the favorable properties of the designed ankyrin repeat protein scaffold, we created a FADA biosensor suitable for imaging of proteins on the cell surface, as well as in the cytosol. Moreover, based on the requirement of dimerization for strong fluorogen activation, a prototype FADA biosensor for in situ detection of a target protein and protein-protein interactions was developed. Therefore, FADAs are versatile fluorescent probes that are easily produced and suitable for diverse applications and thus extend the FAP technology.
		+
		+	Generation of Fluorogen-Activating Designed Ankyrin Repeat Proteins (FADAs) as Versatile Sensor Tools.,Schutz M, Batyuk A, Klenk C, Kummer L, de Picciotto S, Gulbakan B, Wu Y, Newby GA, Zosel F, Schoppe J, Sedlak E, Mittl PR, Zenobi R, Wittrup KD, Pluckthun A J Mol Biol. 2016 Mar 27;428(6):1272-89. doi: 10.1016/j.jmb.2016.01.017. Epub 2016, Jan 23. PMID:26812208<ref>PMID:26812208</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5aao" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:52, 3 February 2016

2016-02-03T15:52:09Z

←Older revision		Revision as of 15:52, 3 February 2016
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of fluorogen-activating designed ankyrin repeat protein (DARPin) dimer in complex with malachite green==
-		+	<StructureSection load='5aao' size='340' side='right' caption='[[5aao]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~The entry~~ 5aao is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5aao]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AAO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AAO FirstGlance]. <br>
-	~~Authors~~: ~~Batyuk~~, A., ~~Schuetz, M~~., ~~Kummer, L~~., ~~Wu, Y~~., ~~Mittl, P~~., ~~Plueckthun, A~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FE:4-[[4-(DIMETHYLAMINO)CYCLOHEXA-2,5-DIEN-1-YLIDENE]-(4-METHOXYPHENYL)METHYL]-N,N-DIMETHYL-ANILINE'>6FE</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=5aao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aao OCA], [http://pdbe.org/5aao PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5aao RCSB], [http://www.ebi.ac.uk/pdbsum/5aao PDBsum]</span></td></tr>
-	~~Description: Crystal structure of fluorogen-activating designed ankyrin repeat protein (DARPin) dimer in complex with malachite green~~	+	</table>
-	[[Category: ~~Unreleased Structures~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Batyuk, A]]
	[[Category: Kummer, L]]		[[Category: Kummer, L]]
-	[[Category: Plueckthun, A]]
	[[Category: Mittl, P]]		[[Category: Mittl, P]]
-	[[Category: Wu, Y]]	+	[[Category: Plueckthun, A]]
	[[Category: Schuetz, M]]		[[Category: Schuetz, M]]
-	[[Category: ~~Batyuk~~, A]]	+	[[Category: Wu, Y]]
		+	[[Category: Fluorescent protein]]
		+	[[Category: Fluorogen-activation]]
		+	[[Category: Homodimer]]
		+	[[Category: Malachite green]]

OCA at 00:25, 1 December 2015

2015-12-01T00:25:56Z

←Older revision		Revision as of 00:25, 1 December 2015
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kummer, L]]		[[Category: Kummer, L]]
-	[[Category: Wu, Y]]
	[[Category: Plueckthun, A]]		[[Category: Plueckthun, A]]
	[[Category: Mittl, P]]		[[Category: Mittl, P]]
		+	[[Category: Wu, Y]]
	[[Category: Schuetz, M]]		[[Category: Schuetz, M]]
	[[Category: Batyuk, A]]		[[Category: Batyuk, A]]

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

2015-08-05T17:35:05Z

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

←Older revision

Revision as of 17:35, 5 August 2015

OCA: New page: '''Unreleased structure''' The entry 5aao is ON HOLD until Paper Publication Authors: Batyuk, A., Schuetz, M., Kummer, L., Wu, Y., Mittl, P., Plueckthun, A. Description: Crystal struct...

2015-08-05T17:35:03Z

New page: '''Unreleased structure''' The entry 5aao is ON HOLD until Paper Publication Authors: Batyuk, A., Schuetz, M., Kummer, L., Wu, Y., Mittl, P., Plueckthun, A. Description: Crystal struct...

New page

'''Unreleased structure'''

The entry 5aao is ON HOLD until Paper Publication

Authors: Batyuk, A., Schuetz, M., Kummer, L., Wu, Y., Mittl, P., Plueckthun, A.

Description: Crystal structure of fluorogen-activating designed ankyrin repeat protein (DARPin) dimer in complex with malachite green
[[Category: Unreleased Structures]]
[[Category: Kummer, L]]
[[Category: Wu, Y]]
[[Category: Plueckthun, A]]
[[Category: Mittl, P]]
[[Category: Schuetz, M]]
[[Category: Batyuk, A]]