7kd1 - Revision history

OCA at 15:21, 18 October 2023

2023-10-18T15:21:37Z

←Older revision		Revision as of 15:21, 18 October 2023
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	<StructureSection load='7kd1' size='340' side='right'caption='[[7kd1]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='7kd1' size='340' side='right'caption='[[7kd1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7kd1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KD1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kd1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_mutans_UA159 Streptococcus mutans UA159]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KD1 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=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]] 1.9Å</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=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=7kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kd1 OCA], [https://pdbe.org/7kd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kd1 RCSB], [https://www.ebi.ac.uk/pdbsum/7kd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kd1 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=7kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kd1 OCA], [https://pdbe.org/7kd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kd1 RCSB], [https://www.ebi.ac.uk/pdbsum/7kd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kd1 ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7kd1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7kd1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Stagno, J R~~]]	+	[[Category: Streptococcus mutans UA159]]
-	[[Category: ~~Wang, Y X~~]]	+	[[Category: Stagno JR]]
-	[[Category: ~~Wilt, H M~~]]	+	[[Category: Wang Y-X]]
-	[[Category: ~~Apo]]~~	+	[[Category: Wilt HM]]
-	~~[[Category: Gene regulation]]~~	+
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 18:07, 10 March 2021

2021-03-10T18:07:13Z

←Older revision		Revision as of 18:07, 10 March 2021
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	==Apo structure of the THF riboswitch aptamer domain==		==Apo structure of the THF riboswitch aptamer domain==
-	<StructureSection load='7kd1' size='340' side='right'caption='[[7kd1]]' scene=''>	+	<StructureSection load='7kd1' size='340' side='right'caption='[[7kd1]], [[Resolution\|resolution]] 1.90Å' 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=7KD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KD1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kd1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KD1 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=7kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kd1 OCA], [https://pdbe.org/7kd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kd1 RCSB], [https://www.ebi.ac.uk/pdbsum/7kd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kd1 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=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=7kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kd1 OCA], [https://pdbe.org/7kd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kd1 RCSB], [https://www.ebi.ac.uk/pdbsum/7kd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kd1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. We have determined a 1.9-A resolution crystal structure of the ligand-free THF riboswitch aptamer. The pseudoknot binding site 'unwinds' in the absence of ligand, whereby the adjacent helical domains (P1, P2, and P3) become disjointed, resulting in rotation and misalignment of the gene-regulatory P1 helix with respect to P3. In contrast, the second binding site at the three-way junction, which is the first to fold, is structurally conserved between apo and holo forms. This suggests a kinetic role for this site, in which binding of the first ligand molecule to the stably folded three-way junction promotes formation of the regulatory pseudoknot site and subsequent binding of the second molecule. As such, these findings provide a molecular basis for both conformational switching and kinetic control.
		+
		+	Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation.,Wilt HM, Yu P, Tan K, Wang YX, Stagno JR J Struct Biol. 2021 Feb 9;213(1):107703. doi: 10.1016/j.jsb.2021.107703. PMID:33571639<ref>PMID:33571639</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kd1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Stagno JR]]	+	[[Category: Stagno, J R]]
-	[[Category: Wang Y-X]]	+	[[Category: Wang, Y X]]
-	[[Category: Wilt HM]]	+	[[Category: Wilt, H M]]
		+	[[Category: Apo]]
		+	[[Category: Gene regulation]]
		+	[[Category: Riboswitch]]
		+	[[Category: Rna]]

OCA at 14:46, 3 March 2021

2021-03-03T14:46:24Z

←Older revision		Revision as of 14:46, 3 March 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7kd1 is ~~ON HOLD until Paper Publication~~	+	==Apo structure of the THF riboswitch aptamer domain==
-		+	<StructureSection load='7kd1' size='340' side='right'caption='[[7kd1]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KD1 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=7kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kd1 OCA], [https://pdbe.org/7kd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kd1 RCSB], [https://www.ebi.ac.uk/pdbsum/7kd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kd1 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Stagno JR]]
		+	[[Category: Wang Y-X]]
		+	[[Category: Wilt HM]]

OCA at 09:24, 3 February 2021

2021-02-03T09:24:28Z

←Older revision		Revision as of 09:24, 3 February 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7kd1 is ON HOLD	+	The entry 7kd1 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 11:10, 16 December 2020

2020-12-16T11:10:05Z

←Older revision		Revision as of 11:10, 16 December 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7kd1 is ON HOLD ~~until Paper Publication~~	+	The entry 7kd1 is ON HOLD

	Authors:		Authors:

OCA at 06:30, 11 November 2020

2020-11-11T06:30:34Z

←Older revision		Revision as of 06:30, 11 November 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7kd1 is ON HOLD	+	The entry 7kd1 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7kd1" [edit=sysop:move=sysop]

2020-10-14T04:25:05Z

Protected "7kd1" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:25, 14 October 2020

OCA: New page: '''Unreleased structure''' The entry 7kd1 is ON HOLD Authors: Description: Category: Unreleased Structures

2020-10-14T04:25:04Z

New page: '''Unreleased structure''' The entry 7kd1 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7kd1 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]