4qk8 - Revision history

OCA at 12:46, 1 March 2024

2024-03-01T12:46:56Z

←Older revision		Revision as of 12:46, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qk8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacter_pseudethanolicus Thermoanaerobacter pseudethanolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QK8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qk8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacter_pseudethanolicus Thermoanaerobacter pseudethanolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QK8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene>, <scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3.05Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene>, <scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [https://pdbe.org/4qk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [https://www.ebi.ac.uk/pdbsum/4qk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qk8 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=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [https://pdbe.org/4qk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [https://www.ebi.ac.uk/pdbsum/4qk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qk8 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Bacterial second messenger cyclic di-AMP (c-di-AMP) is implicated in signaling DNA damage and cell wall stress through interactions with several protein receptors and a widespread ydaO-type riboswitch. We report the crystal structures of c-di-AMP riboswitches from Thermoanaerobacter pseudethanolicus and Thermovirga lienii determined at approximately 3.0-A resolution. In both species, the RNA adopts an unforeseen 'square'-shaped pseudosymmetrical architecture that features two three-way junctions, a turn and a pseudoknot, positioned in the square corners. Uncharacteristically for riboswitches, the structure is stapled by two ligand molecules that span the interior of the structure and employ similar noncanonical interactions for RNA recognition. Mutations in either ligand-binding site negatively affect c-di-AMP binding, suggesting that the riboswitch-triggered genetic response requires contribution of both ligands. Our data provide what are to our knowledge the first insights into specific sensing of c-di-AMP and a molecular mechanism underlying the common c-di-AMP-dependent control of essential cellular processes in bacteria.
-
-	Structural insights into recognition of c-di-AMP by the ydaO riboswitch.,Gao A, Serganov A Nat Chem Biol. 2014 Sep;10(9):787-92. doi: 10.1038/nchembio.1607. Epub 2014 Aug, 3. PMID:25086507<ref>PMID:25086507</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4qk8" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]		*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:33, 15 February 2023

2023-02-15T11:33:19Z

←Older revision		Revision as of 11:33, 15 February 2023
Line 3:		Line 3:
	<StructureSection load='4qk8' size='340' side='right'caption='[[4qk8]], [[Resolution\|resolution]] 3.05Å' scene=''>		<StructureSection load='4qk8' size='340' side='right'caption='[[4qk8]], [[Resolution\|resolution]] 3.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qk8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QK8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QK8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qk8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacter_pseudethanolicus Thermoanaerobacter pseudethanolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QK8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene>, <scene name='pdbligand=K:~~POTASSIUM+ION~~'>K</scene>, <scene name='pdbligand=MG:~~MAGNESIUM~~+ION'>MG</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE~~+ION'>~~SO4~~</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene>, <scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~23G~~:~~GUANOSINE-5-PHOSPHATE-2,3-CYCLIC~~+~~PHOSPHATE~~'>~~23G~~</scene>~~, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [https://pdbe.org/4qk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [https://www.ebi.ac.uk/pdbsum/4qk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qk8 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qk9\|4qk9]], [[4qka\|4qka]]~~</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=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [~~http~~://pdbe.org/4qk8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qk8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qk8 ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 18:

	==See Also==		==See Also==
-	*[[Riboswitch\|Riboswitch]]	+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gao, A~~]]	+	[[Category: Thermoanaerobacter pseudethanolicus]]
-	[[Category: ~~Serganov,~~ A]]	+	[[Category: Gao A]]
-	[[Category: ~~C-di-amp riboswitch]]~~	+	[[Category: Serganov A]]
-	~~[[Category: Rna~~]]	+

OCA at 09:20, 24 April 2019

2019-04-24T09:20:05Z

←Older revision		Revision as of 09:20, 24 April 2019
Line 1:		Line 1:

	==Thermoanaerobacter pseudethanolicus c-di-AMP riboswitch==		==Thermoanaerobacter pseudethanolicus c-di-AMP riboswitch==
-	<StructureSection load='4qk8' size='340' side='right' caption='[[4qk8]], [[Resolution\|resolution]] 3.05Å' scene=''>	+	<StructureSection load='4qk8' size='340' side='right'caption='[[4qk8]], [[Resolution\|resolution]] 3.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qk8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QK8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QK8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qk8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QK8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QK8 FirstGlance]. <br>
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Gao, A]]		[[Category: Gao, A]]
	[[Category: Serganov, A]]		[[Category: Serganov, A]]
	[[Category: C-di-amp riboswitch]]		[[Category: C-di-amp riboswitch]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 14:42, 11 August 2016

2016-08-11T14:42:41Z

←Older revision		Revision as of 14:42, 11 August 2016
Line 1:		Line 1:
		+
	==Thermoanaerobacter pseudethanolicus c-di-AMP riboswitch==		==Thermoanaerobacter pseudethanolicus c-di-AMP riboswitch==
	<StructureSection load='4qk8' size='340' side='right' caption='[[4qk8]], [[Resolution\|resolution]] 3.05Å' scene=''>		<StructureSection load='4qk8' size='340' side='right' caption='[[4qk8]], [[Resolution\|resolution]] 3.05Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qk9\|4qk9]], [[4qka\|4qka]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qk9\|4qk9]], [[4qka\|4qka]]</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=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [http://www.ebi.ac.uk/pdbsum/4qk8 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=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [http://pdbe.org/4qk8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [http://www.ebi.ac.uk/pdbsum/4qk8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qk8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4qk8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch\|Riboswitch]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:24, 20 January 2015

2015-01-20T08:24:08Z

←Older revision		Revision as of 08:24, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qk8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QK8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QK8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qk8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QK8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QK8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qk9\|4qk9]], [[4qka\|4qka]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qk9\|4qk9]], [[4qka\|4qka]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [http://www.ebi.ac.uk/pdbsum/4qk8 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=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [http://www.ebi.ac.uk/pdbsum/4qk8 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Gao, A.]]	+	[[Category: Gao, A]]
-	[[Category: Serganov, A.]]	+	[[Category: Serganov, A]]
	[[Category: C-di-amp riboswitch]]		[[Category: C-di-amp riboswitch]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 05:41, 27 August 2014

2014-08-27T05:41:13Z

←Older revision		Revision as of 05:41, 27 August 2014
Line 8:		Line 8:
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [http://www.ebi.ac.uk/pdbsum/4qk8 PDBsum]</span></td></tr>		<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [http://www.ebi.ac.uk/pdbsum/4qk8 PDBsum]</span></td></tr>
	<table>		<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial second messenger cyclic di-AMP (c-di-AMP) is implicated in signaling DNA damage and cell wall stress through interactions with several protein receptors and a widespread ydaO-type riboswitch. We report the crystal structures of c-di-AMP riboswitches from Thermoanaerobacter pseudethanolicus and Thermovirga lienii determined at approximately 3.0-A resolution. In both species, the RNA adopts an unforeseen 'square'-shaped pseudosymmetrical architecture that features two three-way junctions, a turn and a pseudoknot, positioned in the square corners. Uncharacteristically for riboswitches, the structure is stapled by two ligand molecules that span the interior of the structure and employ similar noncanonical interactions for RNA recognition. Mutations in either ligand-binding site negatively affect c-di-AMP binding, suggesting that the riboswitch-triggered genetic response requires contribution of both ligands. Our data provide what are to our knowledge the first insights into specific sensing of c-di-AMP and a molecular mechanism underlying the common c-di-AMP-dependent control of essential cellular processes in bacteria.
		+
		+	Structural insights into recognition of c-di-AMP by the ydaO riboswitch.,Gao A, Serganov A Nat Chem Biol. 2014 Sep;10(9):787-92. doi: 10.1038/nchembio.1607. Epub 2014 Aug, 3. PMID:25086507<ref>PMID:25086507</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 02:48, 7 August 2014

2014-08-07T02:48:43Z

←Older revision		Revision as of 02:48, 7 August 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Thermoanaerobacter pseudethanolicus c-di-AMP riboswitch==
-		+	<StructureSection load='4qk8' size='340' side='right' caption='[[4qk8]], [[Resolution\|resolution]] 3.05Å' scene=''>
-	~~The entry~~ 4qk8 is ~~ON HOLD~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4qk8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QK8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QK8 FirstGlance]. <br>
-	~~Authors~~: Gao, A., Serganov, A.	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BA:(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D 3,2-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL+5,12-DIOXIDE'>2BA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
-		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
-	~~Description~~:	+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qk9\|4qk9]], [[4qka\|4qka]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qk8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qk8 RCSB], [http://www.ebi.ac.uk/pdbsum/4qk8 PDBsum]</span></td></tr>
		+	<table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gao, A.]]
		+	[[Category: Serganov, A.]]
		+	[[Category: C-di-amp riboswitch]]
		+	[[Category: Rna]]

OCA at 06:50, 9 July 2014

2014-07-09T06:50:21Z

←Older revision		Revision as of 06:50, 9 July 2014
Line 5:		Line 5:
	Authors: Gao, A., Serganov, A.		Authors: Gao, A., Serganov, A.

-	Description: ~~Structure 1~~	+	Description:

OCA: Protected "4qk8" [edit=sysop:move=sysop]

2014-06-11T08:10:02Z

Protected "4qk8" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:10, 11 June 2014

OCA: New page: '''Unreleased structure''' The entry 4qk8 is ON HOLD Authors: Gao, A., Serganov, A. Description: Structure 1

2014-06-11T08:10:00Z

New page: '''Unreleased structure''' The entry 4qk8 is ON HOLD Authors: Gao, A., Serganov, A. Description: Structure 1

New page

'''Unreleased structure'''

The entry 4qk8 is ON HOLD

Authors: Gao, A., Serganov, A.

Description: Structure 1