5fk2 - Revision history

OCA at 11:40, 10 January 2024

OCA — Wed, 10 Jan 2024 11:40:13 GMT

←Older revision		Revision as of 11:40, 10 January 2024
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	</div>		</div>
	<div class="pdbe-citations 5fk2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fk2" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:54, 19 July 2023

OCA — Wed, 19 Jul 2023 06:54:48 GMT

←Older revision		Revision as of 06:54, 19 July 2023
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	<StructureSection load='5fk2' size='340' side='right'caption='[[5fk2]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5fk2' size='340' side='right'caption='[[5fk2]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fk2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FK2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FK2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fk2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis Caldanaerobacter subterraneus subsp. tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FK2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FK2 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=SAM:S-ADENOSYLMETHIONINE'>SAM</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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5fjc\|5fjc]]~~, ~~[[5fk1\|5fk1]], [[5fk3\|5fk3]], [[5fk4\|5fk4]], [[5fk5\|5fk5]], [[5fk6\|5fk6]], [[5fkd\|5fkd]], [[5fke\|5fke]], [[5fkf\|5fkf]], [[5fkg\|5fkg]], [[5fkh\|5fkh]]~~</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=SAM:S-ADENOSYLMETHIONINE'>SAM</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=5fk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fk2 OCA], [~~http~~://pdbe.org/5fk2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fk2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fk2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fk2 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=5fk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fk2 OCA], [https://pdbe.org/5fk2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fk2 RCSB], [https://www.ebi.ac.uk/pdbsum/5fk2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fk2 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: Caldanaerobacter subterraneus subsp. tengcongensis]]
	[[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]]~~	+
-	~~[[Category: Sam-i riboswitch~~]]	+

OCA at 07:23, 6 May 2020

OCA — Wed, 06 May 2020 07:23:10 GMT

←Older revision		Revision as of 07:23, 6 May 2020
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	==SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is GG==		==SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is GG==
-	<StructureSection load='5fk2' size='340' side='right' caption='[[5fk2]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5fk2' size='340' side='right'caption='[[5fk2]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fk2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FK2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FK2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fk2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FK2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FK2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>	+	</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=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fjc\|5fjc]], [[5fk1\|5fk1]], [[5fk3\|5fk3]], [[5fk4\|5fk4]], [[5fk5\|5fk5]], [[5fk6\|5fk6]], [[5fkd\|5fkd]], [[5fke\|5fke]], [[5fkf\|5fkf]], [[5fkg\|5fkg]], [[5fkh\|5fkh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fjc\|5fjc]], [[5fk1\|5fk1]], [[5fk3\|5fk3]], [[5fk4\|5fk4]], [[5fk5\|5fk5]], [[5fk6\|5fk6]], [[5fkd\|5fkd]], [[5fke\|5fke]], [[5fkf\|5fkf]], [[5fkg\|5fkg]], [[5fkh\|5fkh]]</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=5fk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fk2 OCA], [http://pdbe.org/5fk2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fk2 RCSB], [http://www.ebi.ac.uk/pdbsum/5fk2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fk2 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=5fk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fk2 OCA], [http://pdbe.org/5fk2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fk2 RCSB], [http://www.ebi.ac.uk/pdbsum/5fk2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fk2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5fk2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5fk2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__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 17:46, 12 July 2016

OCA — Tue, 12 Jul 2016 17:46:47 GMT

←Older revision		Revision as of 17:46, 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=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fjc\|5fjc]], [[5fk1\|5fk1]], [[5fk3\|5fk3]], [[5fk4\|5fk4]], [[5fk5\|5fk5]], [[5fk6\|5fk6]], [[5fkd\|5fkd]], [[5fke\|5fke]], [[5fkf\|5fkf]], [[5fkg\|5fkg]], [[5fkh\|5fkh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fjc\|5fjc]], [[5fk1\|5fk1]], [[5fk3\|5fk3]], [[5fk4\|5fk4]], [[5fk5\|5fk5]], [[5fk6\|5fk6]], [[5fkd\|5fkd]], [[5fke\|5fke]], [[5fkf\|5fkf]], [[5fkg\|5fkg]], [[5fkh\|5fkh]]</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=5fk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fk2 OCA], [http://pdbe.org/5fk2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fk2 RCSB], [http://www.ebi.ac.uk/pdbsum/5fk2 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=5fk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fk2 OCA], [http://pdbe.org/5fk2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fk2 RCSB], [http://www.ebi.ac.uk/pdbsum/5fk2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fk2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:57, 1 June 2016

OCA — Wed, 01 Jun 2016 22:57:14 GMT

←Older revision		Revision as of 22:57, 1 June 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5fk2 is ~~ON HOLD until Paper~~ Publication	+	==SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is GG==
		+	<StructureSection load='5fk2' size='340' side='right' caption='[[5fk2]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fk2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FK2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FK2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fjc\|5fjc]], [[5fk1\|5fk1]], [[5fk3\|5fk3]], [[5fk4\|5fk4]], [[5fk5\|5fk5]], [[5fk6\|5fk6]], [[5fkd\|5fkd]], [[5fke\|5fke]], [[5fkf\|5fkf]], [[5fkg\|5fkg]], [[5fkh\|5fkh]]</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=5fk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fk2 OCA], [http://pdbe.org/5fk2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fk2 RCSB], [http://www.ebi.ac.uk/pdbsum/5fk2 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: SAM-I riboswitch bearing~~ the H. ~~marismortui Kt-7 variant 3bn is GG~~	+	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 5fk2" 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]]
		+	[[Category: Sam-i riboswitch]]

OCA: Protected "5fk2" [edit=sysop:move=sysop]

OCA — Thu, 22 Oct 2015 04:39:45 GMT

Protected "5fk2" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:39, 22 October 2015

OCA: New page: '''Unreleased structure''' The entry 5fk2 is ON HOLD until Paper Publication Authors: Huang, L., Lilley, D.M.J. Description: SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3b...

OCA — Thu, 22 Oct 2015 04:39:43 GMT

New page: '''Unreleased structure''' The entry 5fk2 is ON HOLD until Paper Publication Authors: Huang, L., Lilley, D.M.J. Description: SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3b...

New page

'''Unreleased structure'''

The entry 5fk2 is ON HOLD until Paper Publication

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

Description: SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is GG
[[Category: Unreleased Structures]]
[[Category: Lilley, D.M.J]]
[[Category: Huang, L]]