7u0y - Revision history

OCA at 17:10, 18 October 2023

OCA — Wed, 18 Oct 2023 17:10:08 GMT

←Older revision		Revision as of 17:10, 18 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7u0y]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] 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=7U0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U0Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[7u0y]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] 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=7U0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U0Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=KY6:4-[(Z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile'>KY6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.66Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=KY6:4-[(Z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile'>KY6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7u0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0y OCA], [https://pdbe.org/7u0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0y RCSB], [https://www.ebi.ac.uk/pdbsum/7u0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0y 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=7u0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0y OCA], [https://pdbe.org/7u0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0y RCSB], [https://www.ebi.ac.uk/pdbsum/7u0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0y ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7u0y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7u0y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:26, 7 September 2022

OCA — Wed, 07 Sep 2022 19:26:59 GMT

←Older revision		Revision as of 19:26, 7 September 2022
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-	====	+	==Crystal structure of Pepper RNA aptamer in complex with HBC599 ligand and Fab BL3-6==
-	<StructureSection load='7u0y' size='340' side='right'caption='[[7u0y]]' scene=''>	+	<StructureSection load='7u0y' size='340' side='right'caption='[[7u0y]], [[Resolution\|resolution]] 2.66Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7u0y]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] 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=7U0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U0Y 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=7u0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0y OCA], [https://pdbe.org/7u0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0y RCSB], [https://www.ebi.ac.uk/pdbsum/7u0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0y 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=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=KY6:4-[(Z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile'>KY6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7u0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0y OCA], [https://pdbe.org/7u0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0y RCSB], [https://www.ebi.ac.uk/pdbsum/7u0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0y ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl (HBC) derivatives with tight affinity and activates their fluorescence. To investigate how Pepper RNA folds to create a binding site for HBC, we used antibody-assisted crystallography to determine the structures of Pepper bound to HBC530 and HBC599 to 2.3 and 2.7 A resolutions, respectively. The structural data show that Pepper folds into an elongated structure and organizes nucleotides within an internal bulge to create the ligand binding site, assisted by an out-of-plane platform created by tertiary interactions with an adjacent bulge. As predicted from a lack of K(+) dependence, Pepper does not use a G-quadruplex to form a binding pocket for HBC. Instead, Pepper uses a unique base-quadruple.base-triple stack to sandwich the ligand with a U.G wobble pair. Site-bound Mg(2+) ions support ligand binding structurally and energetically. This research provides insight into the structural features that allow the Pepper aptamer to bind HBC and show how Pepper's function may expand to allow the in vivo detection of other small molecules and metals.
		+
		+	Structural Basis for Fluorescence Activation by Pepper RNA.,Rees HC, Gogacz W, Li NS, Koirala D, Piccirilli JA ACS Chem Biol. 2022 Jul 15;17(7):1866-1875. doi: 10.1021/acschembio.2c00290. Epub, 2022 Jun 27. PMID:35759696<ref>PMID:35759696</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7u0y" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Mus musculus]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Piccirilli JA]]
		+	[[Category: Rees HC]]

OCA at 06:37, 31 August 2022

OCA — Wed, 31 Aug 2022 06:37:04 GMT

←Older revision		Revision as of 06:37, 31 August 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7u0y ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7u0y' size='340' side='right'caption='[[7u0y]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</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=7u0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0y OCA], [https://pdbe.org/7u0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0y RCSB], [https://www.ebi.ac.uk/pdbsum/7u0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0y ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 09:29, 30 March 2022

OCA — Wed, 30 Mar 2022 09:29:42 GMT

←Older revision		Revision as of 09:29, 30 March 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7u0y is ON HOLD	+	The entry 7u0y is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7u0y" [edit=sysop:move=sysop]

OCA — Wed, 02 Mar 2022 05:06:50 GMT

Protected "7u0y" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:06, 2 March 2022

OCA: New page: '''Unreleased structure''' The entry 7u0y is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Mar 2022 05:06:49 GMT

New page: '''Unreleased structure''' The entry 7u0y is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7u0y is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]