7szu - Revision history

OCA at 16:56, 18 October 2023

OCA — Wed, 18 Oct 2023 16:56:27 GMT

←Older revision		Revision as of 16:56, 18 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7szu]] 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=7SZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SZU FirstGlance]. <br>		<table><tr><td colspan='2'>[[7szu]] 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=7SZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SZU 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=J8F:4-[(~{Z})-1-cyano-2-[4-[2-hydroxyethyl(methyl)amino]phenyl]ethenyl]benzenecarbonitrile'>J8F</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.24Å</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=J8F:4-[(~{Z})-1-cyano-2-[4-[2-hydroxyethyl(methyl)amino]phenyl]ethenyl]benzenecarbonitrile'>J8F</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7szu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7szu OCA], [https://pdbe.org/7szu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7szu RCSB], [https://www.ebi.ac.uk/pdbsum/7szu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7szu 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=7szu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7szu OCA], [https://pdbe.org/7szu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7szu RCSB], [https://www.ebi.ac.uk/pdbsum/7szu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7szu ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7szu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7szu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:45, 8 September 2022

OCA — Thu, 08 Sep 2022 04:45:36 GMT

←Older revision		Revision as of 04:45, 8 September 2022
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-	====	+	==Crystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6==
-	<StructureSection load='7szu' size='340' side='right'caption='[[7szu]]' scene=''>	+	<StructureSection load='7szu' size='340' side='right'caption='[[7szu]], [[Resolution\|resolution]] 2.24Å' 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'>[[7szu]] 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=7SZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SZU 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=7szu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7szu OCA], [https://pdbe.org/7szu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7szu RCSB], [https://www.ebi.ac.uk/pdbsum/7szu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7szu 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=J8F:4-[(~{Z})-1-cyano-2-[4-[2-hydroxyethyl(methyl)amino]phenyl]ethenyl]benzenecarbonitrile'>J8F</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7szu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7szu OCA], [https://pdbe.org/7szu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7szu RCSB], [https://www.ebi.ac.uk/pdbsum/7szu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7szu 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 7szu" 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 16:13, 6 July 2022

OCA — Wed, 06 Jul 2022 16:13:58 GMT

←Older revision		Revision as of 16:13, 6 July 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7szu ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7szu' size='340' side='right'caption='[[7szu]]' 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=7szu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7szu OCA], [https://pdbe.org/7szu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7szu RCSB], [https://www.ebi.ac.uk/pdbsum/7szu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7szu ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 03:50, 15 June 2022

OCA — Wed, 15 Jun 2022 03:50:20 GMT

←Older revision		Revision as of 03:50, 15 June 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7szu is ON HOLD ~~until Paper Publication~~	+	The entry 7szu is ON HOLD

	Authors:		Authors:

OCA at 05:01, 2 March 2022

OCA — Wed, 02 Mar 2022 05:01:20 GMT

←Older revision		Revision as of 05:01, 2 March 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 08 Dec 2021 08:36:02 GMT

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

←Older revision

Revision as of 08:36, 8 December 2021

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

OCA — Wed, 08 Dec 2021 08:36:01 GMT

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

New page

'''Unreleased structure'''

The entry 7szu is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]