6vui - Revision history

OCA at 08:20, 11 October 2023

OCA — Wed, 11 Oct 2023 08:20:31 GMT

←Older revision		Revision as of 08:20, 11 October 2023
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	<StructureSection load='6vui' size='340' side='right'caption='[[6vui]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='6vui' size='340' side='right'caption='[[6vui]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vui]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VUI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vui]] 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=6VUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VUI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>~~, ~~<scene name='pdbligand=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</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]] 2.681Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3q50\|3q50]]~~, ~~[[3q51\|3q51]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</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=6vui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vui OCA], [https://pdbe.org/6vui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vui RCSB], [https://www.ebi.ac.uk/pdbsum/6vui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vui 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=6vui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vui OCA], [https://pdbe.org/6vui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vui RCSB], [https://www.ebi.ac.uk/pdbsum/6vui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vui ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jenkins~~, J L~~]]	+	[[Category: Jenkins JL]]
-	[[Category: Wedekind~~, J E]]~~	+	[[Category: Wedekind JE]]
-	~~[[Category: Aptamer]]~~	+
-	~~[[Category: H-type]]~~	+
-	~~[[Category: Metabolite]]~~	+
-	~~[[Category: Preq0]]~~	+
-	~~[[Category: Preq1]]~~	+
-	~~[[Category: Pseudoknot]]~~	+
-	~~[[Category: Queuosine]]~~	+
-	~~[[Category: Ribosomal binding site]]~~	+
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 07:11, 16 March 2022

OCA — Wed, 16 Mar 2022 07:11:56 GMT

←Older revision		Revision as of 07:11, 16 March 2022
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	<StructureSection load='6vui' size='340' side='right'caption='[[6vui]], [[Resolution\|resolution]] 2.68Å' scene=''>		<StructureSection load='6vui' size='340' side='right'caption='[[6vui]], [[Resolution\|resolution]] 2.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vui]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VUI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VUI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vui]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VUI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3q50\|3q50]], [[3q51\|3q51]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3q50\|3q50]], [[3q51\|3q51]]</div></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=6vui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vui OCA], [~~http~~://pdbe.org/6vui PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vui RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vui PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vui 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=6vui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vui OCA], [https://pdbe.org/6vui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vui RCSB], [https://www.ebi.ac.uk/pdbsum/6vui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vui 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 6vui" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6vui" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:35, 26 August 2020

OCA — Wed, 26 Aug 2020 11:35:21 GMT

←Older revision		Revision as of 11:35, 26 August 2020
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vui OCA], [http://pdbe.org/6vui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vui RCSB], [http://www.ebi.ac.uk/pdbsum/6vui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vui 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=6vui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vui OCA], [http://pdbe.org/6vui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vui RCSB], [http://www.ebi.ac.uk/pdbsum/6vui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vui ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 A and 2.65 A-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1-exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1-sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.
		+
		+	Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.,Schroeder GM, Dutta D, Cavender CE, Jenkins JL, Pritchett EM, Baker CD, Ashton JM, Mathews DH, Wedekind JE Nucleic Acids Res. 2020 Aug 20;48(14):8146-8164. doi: 10.1093/nar/gkaa546. PMID:32597951<ref>PMID:32597951</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6vui" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:38, 8 July 2020

OCA — Wed, 08 Jul 2020 14:38:54 GMT

←Older revision		Revision as of 14:38, 8 July 2020
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	==Metabolite-bound PreQ1 riboswitch with Mn2+==		==Metabolite-bound PreQ1 riboswitch with Mn2+==
-	<StructureSection load='6vui' size='340' side='right'caption='[[6vui]]' scene=''>	+	<StructureSection load='6vui' size='340' side='right'caption='[[6vui]], [[Resolution\|resolution]] 2.68Å' 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=6VUI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VUI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vui]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VUI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VUI FirstGlance]. <br>
-	</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=6vui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vui OCA], [http://pdbe.org/6vui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vui RCSB], [http://www.ebi.ac.uk/pdbsum/6vui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vui 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PRF:7-DEAZA-7-AMINOMETHYL-GUANINE'>PRF</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3q50\|3q50]], [[3q51\|3q51]]</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=6vui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vui OCA], [http://pdbe.org/6vui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vui RCSB], [http://www.ebi.ac.uk/pdbsum/6vui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vui ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jenkins JL]]	+	[[Category: Jenkins, J L]]
-	[[Category: ~~Wededkind JE~~]]	+	[[Category: Wedekind, J E]]
		+	[[Category: Aptamer]]
		+	[[Category: H-type]]
		+	[[Category: Metabolite]]
		+	[[Category: Preq0]]
		+	[[Category: Preq1]]
		+	[[Category: Pseudoknot]]
		+	[[Category: Queuosine]]
		+	[[Category: Ribosomal binding site]]
		+	[[Category: Riboswitch]]
		+	[[Category: Rna]]

OCA at 06:26, 25 June 2020

OCA — Thu, 25 Jun 2020 06:26:03 GMT

←Older revision		Revision as of 06:26, 25 June 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6vui ~~is ON HOLD until Paper Publication~~	+	==Metabolite-bound PreQ1 riboswitch with Mn2+==
-		+	<StructureSection load='6vui' size='340' side='right'caption='[[6vui]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VUI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VUI FirstGlance]. <br>
-	~~Description~~:	+	</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=6vui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vui OCA], [http://pdbe.org/6vui PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vui RCSB], [http://www.ebi.ac.uk/pdbsum/6vui PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vui ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Jenkins JL]]
		+	[[Category: Wededkind JE]]

OCA at 06:04, 11 March 2020

OCA — Wed, 11 Mar 2020 06:04:09 GMT

←Older revision		Revision as of 06:04, 11 March 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6vui is ON HOLD	+	The entry 6vui is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6vui" [edit=sysop:move=sysop]

OCA — Wed, 26 Feb 2020 08:10:21 GMT

Protected "6vui" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:10, 26 February 2020

OCA: New page: '''Unreleased structure''' The entry 6vui is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Feb 2020 08:10:19 GMT

New page: '''Unreleased structure''' The entry 6vui is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6vui is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]