8ami - Revision history

OCA at 08:12, 7 February 2024

OCA — Wed, 07 Feb 2024 08:12:39 GMT

←Older revision		Revision as of 08:12, 7 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8ami]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AMI FirstGlance]. <br>		<table><tr><td colspan='2'>[[8ami]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AMI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</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]] 1.79Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</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=8ami FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ami OCA], [https://pdbe.org/8ami PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ami RCSB], [https://www.ebi.ac.uk/pdbsum/8ami PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ami 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=8ami FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ami OCA], [https://pdbe.org/8ami PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ami RCSB], [https://www.ebi.ac.uk/pdbsum/8ami PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ami ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The self-complementary triplet 5'UGG3'/5'UGG3' is a particular structural motif containing noncanonical G-G pair and two U.G wobble pairs. It constitutes a specific structural and electrostatic environment attracting metal ions, particularly Ba2+ ions. Crystallographic research has shown that two Ba2+ cations are located in the major groove of the helix and interact directly with the UGG triplet. A comparison with the unliganded structure has revealed global changes in the RNA structure in the presence of metal ions, whereas thermodynamic measurements have shown increased stability. Moreover, in the structure with Ba2+, an unusual noncanonical G(syn)-G(syn) pair is observed instead of the common G(anti)-G(syn). We further elucidate the metal binding properties of the UGG/UGG triplet by performing crystallographic and thermodynamic studies using DSC and UV melting with other metal ions. The results explain the preferences of the UGG sequence for Ba2+ cations and point to possible applications of this metal-binding propensity.
-
-	Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.,Kiliszek A, Pluta M, Bejger M, Rypniewski W RNA. 2022 Nov 1:rna.079414.122. doi: 10.1261/rna.079414.122. PMID:36319090<ref>PMID:36319090</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8ami" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:13, 24 November 2022

OCA — Thu, 24 Nov 2022 10:13:41 GMT

←Older revision		Revision as of 10:13, 24 November 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 8ami is ~~ON HOLD~~	+	==Crystal structure of AUGUGGCAU duplex with barium ions (model 2)==
		+	<StructureSection load='8ami' size='340' side='right'caption='[[8ami]], [[Resolution\|resolution]] 1.79Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8ami]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AMI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</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=8ami FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ami OCA], [https://pdbe.org/8ami PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ami RCSB], [https://www.ebi.ac.uk/pdbsum/8ami PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ami ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The self-complementary triplet 5'UGG3'/5'UGG3' is a particular structural motif containing noncanonical G-G pair and two U.G wobble pairs. It constitutes a specific structural and electrostatic environment attracting metal ions, particularly Ba2+ ions. Crystallographic research has shown that two Ba2+ cations are located in the major groove of the helix and interact directly with the UGG triplet. A comparison with the unliganded structure has revealed global changes in the RNA structure in the presence of metal ions, whereas thermodynamic measurements have shown increased stability. Moreover, in the structure with Ba2+, an unusual noncanonical G(syn)-G(syn) pair is observed instead of the common G(anti)-G(syn). We further elucidate the metal binding properties of the UGG/UGG triplet by performing crystallographic and thermodynamic studies using DSC and UV melting with other metal ions. The results explain the preferences of the UGG sequence for Ba2+ cations and point to possible applications of this metal-binding propensity.

-	~~Authors~~: ~~Kiliszek~~, A., ~~Rypniewski~~, W.	+	Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.,Kiliszek A, Pluta M, Bejger M, Rypniewski W RNA. 2022 Nov 1:rna.079414.122. doi: 10.1261/rna.079414.122. PMID:36319090<ref>PMID:36319090</ref>

-	~~Description: Crystal structure~~ of ~~AUGUGGCAU duplex with barium ions (model 2)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Rypniewski, W~~]]	+	<div class="pdbe-citations 8ami" style="background-color:#fffaf0;"></div>
-	[[Category: Kiliszek, A]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Kiliszek A]]
		+	[[Category: Rypniewski W]]

OCA: Protected "8ami" [edit=sysop:move=sysop]

OCA — Wed, 10 Aug 2022 03:57:58 GMT

Protected "8ami" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:57, 10 August 2022

OCA: New page: '''Unreleased structure''' The entry 8ami is ON HOLD Authors: Kiliszek, A., Rypniewski, W. Description: Crystal structure of AUGUGGCAU duplex with barium ions (model 2) [[Category: Unr...

OCA — Wed, 10 Aug 2022 03:57:57 GMT

New page: '''Unreleased structure''' The entry 8ami is ON HOLD Authors: Kiliszek, A., Rypniewski, W. Description: Crystal structure of AUGUGGCAU duplex with barium ions (model 2) [[Category: Unr...

New page

'''Unreleased structure'''

The entry 8ami is ON HOLD

Authors: Kiliszek, A., Rypniewski, W.

Description: Crystal structure of AUGUGGCAU duplex with barium ions (model 2)
[[Category: Unreleased Structures]]
[[Category: Rypniewski, W]]
[[Category: Kiliszek, A]]