5fj1 - Revision history

OCA at 06:53, 19 July 2023

OCA — Wed, 19 Jul 2023 06:53:23 GMT

←Older revision		Revision as of 06:53, 19 July 2023
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	<StructureSection load='5fj1' size='340' side='right'caption='[[5fj1]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='5fj1' size='340' side='right'caption='[[5fj1]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fj1]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FJ1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FJ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fj1]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FJ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FJ1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 2.75Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5fj0\|5fj0]]~~, ~~[[5fj4\|5fj4]], [[5fjc\|5fjc]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5fj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fj1 OCA], [~~http~~://pdbe.org/5fj1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fj1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fj1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fj1 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=5fj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fj1 OCA], [https://pdbe.org/5fj1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fj1 RCSB], [https://www.ebi.ac.uk/pdbsum/5fj1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fj1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Haloarcula marismortui]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Huang, L]]	+	[[Category: Huang L]]
-	[[Category: Lilley~~, D M.J]]~~	+	[[Category: Lilley DMJ]]
-	~~[[Category: Kink turn]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna motif~~]]	+

OCA at 07:21, 6 May 2020

OCA — Wed, 06 May 2020 07:21:41 GMT

←Older revision		Revision as of 07:21, 6 May 2020
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	==Structure of the standard kink turn HmKt-7 as stem loop in P212121 space group==		==Structure of the standard kink turn HmKt-7 as stem loop in P212121 space group==
-	<StructureSection load='5fj1' size='340' side='right' caption='[[5fj1]], [[Resolution\|resolution]] 2.75Å' scene=''>	+	<StructureSection load='5fj1' size='340' side='right'caption='[[5fj1]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fj1]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FJ1 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FJ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fj1]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FJ1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FJ1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fj0\|5fj0]], [[5fj4\|5fj4]], [[5fjc\|5fjc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fj0\|5fj0]], [[5fj4\|5fj4]], [[5fjc\|5fjc]]</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=5fj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fj1 OCA], [http://pdbe.org/5fj1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fj1 RCSB], [http://www.ebi.ac.uk/pdbsum/5fj1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fj1 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=5fj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fj1 OCA], [http://pdbe.org/5fj1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fj1 RCSB], [http://www.ebi.ac.uk/pdbsum/5fj1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fj1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Huang, L]]		[[Category: Huang, L]]
	[[Category: Lilley, D M.J]]		[[Category: Lilley, D M.J]]

OCA at 18:31, 12 July 2016

OCA — Tue, 12 Jul 2016 18:31:53 GMT

←Older revision		Revision as of 18:31, 12 July 2016
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fj0\|5fj0]], [[5fj4\|5fj4]], [[5fjc\|5fjc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fj0\|5fj0]], [[5fj4\|5fj4]], [[5fjc\|5fjc]]</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=5fj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fj1 OCA], [http://pdbe.org/5fj1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fj1 RCSB], [http://www.ebi.ac.uk/pdbsum/5fj1 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=5fj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fj1 OCA], [http://pdbe.org/5fj1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fj1 RCSB], [http://www.ebi.ac.uk/pdbsum/5fj1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fj1 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:56, 1 June 2016

OCA — Wed, 01 Jun 2016 22:56:59 GMT

←Older revision		Revision as of 22:56, 1 June 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5fj1 is ~~ON HOLD until Paper~~ Publication	+	==Structure of the standard kink turn HmKt-7 as stem loop in P212121 space group==
		+	<StructureSection load='5fj1' size='340' side='right' caption='[[5fj1]], [[Resolution\|resolution]] 2.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fj1]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FJ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FJ1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fj0\|5fj0]], [[5fj4\|5fj4]], [[5fjc\|5fjc]]</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=5fj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fj1 OCA], [http://pdbe.org/5fj1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fj1 RCSB], [http://www.ebi.ac.uk/pdbsum/5fj1 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	k-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core. We show here that this is determined by the basepair adjacent to the critical G*A pairs. We determined crystal structures of a series of Kt-7 variants in which this 3b,3n position has been systematically varied, showing that this leads to a switch in the conformation. We have previously shown that the 3b,3n position also determines the folding characteristics of the k-turn, i.e. whether or not the k-turn can fold in the presence of metal ions alone. We have analyzed the distribution of 3b,3n sequences from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation of properties for a given k-turn type. We thus demonstrate a strong association between biological function, 3b,3n sequence and k-turn folding and conformation. This has strong predictive power, and can be applied to the modeling of large RNA architectures.

-	~~Authors: Huang~~, L., ~~Lilley~~, D.M.J.	+	A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function.,Huang L, Wang J, Lilley DM Nucleic Acids Res. 2016 Mar 25. pii: gkw201. PMID:27016741<ref>PMID:27016741</ref>

-	~~Description: Structure~~ of the ~~standard kink turn HmKt-7 as stem loop in P212121 space group~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Lilley, D.M.J]]~~	+	<div class="pdbe-citations 5fj1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Huang, L]]		[[Category: Huang, L]]
		+	[[Category: Lilley, D M.J]]
		+	[[Category: Kink turn]]
		+	[[Category: Rna]]
		+	[[Category: Rna motif]]

OCA: Protected "5fj1" [edit=sysop:move=sysop]

OCA — Fri, 16 Oct 2015 03:05:20 GMT

Protected "5fj1" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:05, 16 October 2015

OCA: New page: '''Unreleased structure''' The entry 5fj1 is ON HOLD until Paper Publication Authors: Huang, L., Lilley, D.M.J. Description: Structure of the standard kink turn HmKt-7 as stem loop in ...

OCA — Fri, 16 Oct 2015 03:05:18 GMT

New page: '''Unreleased structure''' The entry 5fj1 is ON HOLD until Paper Publication Authors: Huang, L., Lilley, D.M.J. Description: Structure of the standard kink turn HmKt-7 as stem loop in ...

New page

'''Unreleased structure'''

The entry 5fj1 is ON HOLD until Paper Publication

Authors: Huang, L., Lilley, D.M.J.

Description: Structure of the standard kink turn HmKt-7 as stem loop in P212121 space group
[[Category: Unreleased Structures]]
[[Category: Lilley, D.M.J]]
[[Category: Huang, L]]