7tdb - Revision history

OCA at 17:03, 18 October 2023

OCA — Wed, 18 Oct 2023 17:03:38 GMT

←Older revision		Revision as of 17:03, 18 October 2023
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	<StructureSection load='7tdb' size='340' side='right'caption='[[7tdb]], [[Resolution\|resolution]] 2.56Å' scene=''>		<StructureSection load='7tdb' size='340' side='right'caption='[[7tdb]], [[Resolution\|resolution]] 2.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7tdb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TDB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7tdb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TDB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMI:[2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethoxy-oxidanyl-phosphoryl]methylphosphonic+acid'>GMI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN~~</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]] 2.56Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A23:ADENOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>A23~~</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A23:ADENOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>A23</scene>, <scene name='pdbligand=GMI:[2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethoxy-oxidanyl-phosphoryl]methylphosphonic+acid'>GMI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=7tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tdb OCA], [https://pdbe.org/7tdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tdb RCSB], [https://www.ebi.ac.uk/pdbsum/7tdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tdb 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=7tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tdb OCA], [https://pdbe.org/7tdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tdb RCSB], [https://www.ebi.ac.uk/pdbsum/7tdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tdb ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7tdb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7tdb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Nuthanakanti, A]]	+	[[Category: Nuthanakanti A]]
-	[[Category: Serganov, A]]	+	[[Category: Serganov A]]
-	~~[[Category: Rna~~]]	+

OCA at 07:32, 2 March 2022

OCA — Wed, 02 Mar 2022 07:32:53 GMT

←Older revision		Revision as of 07:32, 2 March 2022
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	==Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, manganese ions==		==Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, manganese ions==
-	<StructureSection load='7tdb' size='340' side='right'caption='[[7tdb]]' scene=''>	+	<StructureSection load='7tdb' size='340' side='right'caption='[[7tdb]], [[Resolution\|resolution]] 2.56Å' 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=7TDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TDB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7tdb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TDB FirstGlance]. <br>
-	</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=7tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tdb OCA], [https://pdbe.org/7tdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tdb RCSB], [https://www.ebi.ac.uk/pdbsum/7tdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tdb 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=GMI:[2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethoxy-oxidanyl-phosphoryl]methylphosphonic+acid'>GMI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A23:ADENOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>A23</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=7tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tdb OCA], [https://pdbe.org/7tdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tdb RCSB], [https://www.ebi.ac.uk/pdbsum/7tdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tdb ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RNA molecules can show high levels of cooperativity in their global folding and interactions with divalent ions. However, cooperativity at individual ligand-RNA interaction sites remains poorly understood. Here, we investigated the binding of thiamine and methylene diphosphonic acid (MDP, a soluble structural analogue of pyrophosphate) to the thiamine pyrophosphate riboswitch. These ligands each bind weakly at proximal subsites, with 10 muM and 1 mM affinities, respectively. The affinity of MDP moderately improves when thiamine or thiamine-like fragments are pre-bound to the RNA. Covalent linking of thiamine and MDP substantially increases riboswitch binding to a notable high affinity of 20 nM. Crystal structures and single-molecule correlated chemical probing revealed favorable induced fit effects upon binding of individual ligands and, unexpectedly, a substantial thermodynamically unfavorable RNA structural rearrangement upon binding of the linked thiamine-MDP ligand. Thus, linking of two ligands of modest affinity, accompanied by an unfavorable structural rearrangement, still yields a potent linked RNA-binding compound. Since complex ligands often bind riboswitches and other RNAs at proximal subsites, principles derived from this work inform and support fragment-linking strategies for identifying small molecules that interact with RNA specifically and with high affinity.
		+
		+	Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery.,Zeller MJ, Nuthanakanti A, Li K, Aube J, Serganov A, Weeks KM ACS Chem Biol. 2022 Jan 21. doi: 10.1021/acschembio.1c00880. PMID:35060698<ref>PMID:35060698</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7tdb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Nuthanakanti A]]	+	[[Category: Nuthanakanti, A]]
-	[[Category: Serganov A]]	+	[[Category: Serganov, A]]
		+	[[Category: Rna]]

OCA at 10:18, 16 February 2022

OCA — Wed, 16 Feb 2022 10:18:30 GMT

←Older revision		Revision as of 10:18, 16 February 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7tdb ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, manganese ions==
-		+	<StructureSection load='7tdb' size='340' side='right'caption='[[7tdb]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TDB FirstGlance]. <br>
-	~~Description~~:	+	</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=7tdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tdb OCA], [https://pdbe.org/7tdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tdb RCSB], [https://www.ebi.ac.uk/pdbsum/7tdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tdb ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Nuthanakanti A]]
		+	[[Category: Serganov A]]

OCA at 05:58, 19 January 2022

OCA — Wed, 19 Jan 2022 05:58:23 GMT

←Older revision		Revision as of 05:58, 19 January 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7tdb is ON HOLD	+	The entry 7tdb is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7tdb" [edit=sysop:move=sysop]

OCA — Wed, 05 Jan 2022 09:22:32 GMT

Protected "7tdb" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:22, 5 January 2022

OCA: New page: '''Unreleased structure''' The entry 7tdb is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Jan 2022 09:22:31 GMT

New page: '''Unreleased structure''' The entry 7tdb is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7tdb is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]