5gwq - Revision history

OCA at 07:23, 1 May 2024

OCA — Wed, 01 May 2024 07:23:24 GMT

←Older revision		Revision as of 07:23, 1 May 2024
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	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5gwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gwq OCA], [https://pdbe.org/5gwq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gwq RCSB], [https://www.ebi.ac.uk/pdbsum/5gwq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gwq 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=5gwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gwq OCA], [https://pdbe.org/5gwq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gwq RCSB], [https://www.ebi.ac.uk/pdbsum/5gwq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gwq ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The non-B DNA structures formed by short tandem repeats on the nascent strand during DNA replication have been proposed to be the structural intermediates that lead to repeat expansion mutations. Tetranucleotide TTTA and CCTG repeat expansions have been known to cause reduction in biofilm formation in Staphylococcus aureus and myotonic dystrophy type 2 in human, respectively. In this study, we report the first three-dimensional minidumbbell (MDB) structure formed by natural DNA sequences containing two TTTA or CCTG repeats. The formation of MDB provides possible pathways for strand slippage to occur, which ultimately leads to repair escape and thus expansion mutations. Our result here shows that MDB is a highly compact structure composed of two type II loops. In addition to the typical stabilizing interactions in type II loops, MDB shows extensive stabilizing forces between the two loops, including two distinctive modes of interactions between the minor groove residues. The formation of MDB enriches the structural diversity of natural DNA sequences, reveals the importance of loop-loop interactions in unusual DNA structures, and provides insights into novel mechanistic pathways of DNA repeat expansion mutations.
-
-	Minidumbbell: A New Form of Native DNA Structure.,Guo P, Lam SL J Am Chem Soc. 2016 Sep 28;138(38):12534-40. doi: 10.1021/jacs.6b06897. Epub 2016, Sep 16. PMID:27589409<ref>PMID:27589409</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5gwq" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:44, 2 August 2023

OCA — Wed, 02 Aug 2023 11:44:51 GMT

←Older revision		Revision as of 11:44, 2 August 2023
Line 1:		Line 1:

	==Structure of two TTTA repeats==		==Structure of two TTTA repeats==
-	<StructureSection load='5gwq' size='340' side='right'caption='[[5gwq~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5gwq' size='340' side='right'caption='[[5gwq]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gwq]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GWQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GWQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gwq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GWQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GWQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5gwl\|5gwl]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=5gwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gwq OCA], [~~http~~://pdbe.org/5gwq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gwq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gwq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gwq 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=5gwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gwq OCA], [https://pdbe.org/5gwq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gwq RCSB], [https://www.ebi.ac.uk/pdbsum/5gwq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gwq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Guo, P~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: ~~Lam, S L~~]]	+	[[Category: Guo P]]
-	[[Category: ~~Dna]]~~	+	[[Category: Lam SL]]
-	~~[[Category: Minidumbbell]]~~	+
-	~~[[Category: Type ii loop~~]]	+

OCA at 06:45, 20 May 2020

OCA — Wed, 20 May 2020 06:45:21 GMT

←Older revision		Revision as of 06:45, 20 May 2020
Line 1:		Line 1:

	==Structure of two TTTA repeats==		==Structure of two TTTA repeats==
-	<StructureSection load='5gwq' size='340' side='right' caption='[[5gwq]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5gwq' size='340' side='right'caption='[[5gwq]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gwq]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GWQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GWQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gwq]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GWQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GWQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gwl\|5gwl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gwl\|5gwl]]</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=5gwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gwq OCA], [http://pdbe.org/5gwq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gwq RCSB], [http://www.ebi.ac.uk/pdbsum/5gwq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gwq 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=5gwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gwq OCA], [http://pdbe.org/5gwq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gwq RCSB], [http://www.ebi.ac.uk/pdbsum/5gwq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gwq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Guo, P]]		[[Category: Guo, P]]
	[[Category: Lam, S L]]		[[Category: Lam, S L]]

OCA at 17:39, 19 October 2016

OCA — Wed, 19 Oct 2016 17:39:47 GMT

←Older revision		Revision as of 17:39, 19 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gwq is ~~ON HOLD~~	+	==Structure of two TTTA repeats==
		+	<StructureSection load='5gwq' size='340' side='right' caption='[[5gwq]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gwq]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GWQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GWQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gwl\|5gwl]]</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=5gwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gwq OCA], [http://pdbe.org/5gwq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gwq RCSB], [http://www.ebi.ac.uk/pdbsum/5gwq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gwq ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The non-B DNA structures formed by short tandem repeats on the nascent strand during DNA replication have been proposed to be the structural intermediates that lead to repeat expansion mutations. Tetranucleotide TTTA and CCTG repeat expansions have been known to cause reduction in biofilm formation in Staphylococcus aureus and myotonic dystrophy type 2 in human, respectively. In this study, we report the first three-dimensional minidumbbell (MDB) structure formed by natural DNA sequences containing two TTTA or CCTG repeats. The formation of MDB provides possible pathways for strand slippage to occur, which ultimately leads to repair escape and thus expansion mutations. Our result here shows that MDB is a highly compact structure composed of two type II loops. In addition to the typical stabilizing interactions in type II loops, MDB shows extensive stabilizing forces between the two loops, including two distinctive modes of interactions between the minor groove residues. The formation of MDB enriches the structural diversity of natural DNA sequences, reveals the importance of loop-loop interactions in unusual DNA structures, and provides insights into novel mechanistic pathways of DNA repeat expansion mutations.

-	~~Authors~~: ~~Guo~~, P., Lam~~, S~~.L.	+	Minidumbbell: A New Form of Native DNA Structure.,Guo P, Lam SL J Am Chem Soc. 2016 Sep 28;138(38):12534-40. doi: 10.1021/jacs.6b06897. Epub 2016, Sep 16. PMID:27589409<ref>PMID:27589409</ref>

-	~~Description: Structure~~ of ~~two TTTA repeats~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5gwq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Guo, P]]		[[Category: Guo, P]]
-	[[Category: Lam, S.L]]	+	[[Category: Lam, S L]]
		+	[[Category: Dna]]
		+	[[Category: Minidumbbell]]
		+	[[Category: Type ii loop]]

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

OCA — Wed, 21 Sep 2016 08:43:55 GMT

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

←Older revision

Revision as of 08:43, 21 September 2016

OCA: New page: '''Unreleased structure''' The entry 5gwq is ON HOLD Authors: Guo, P., Lam, S.L. Description: Structure of two TTTA repeats Category: Unreleased Structures Category: Guo, P [[C...

OCA — Wed, 21 Sep 2016 08:43:54 GMT

New page: '''Unreleased structure''' The entry 5gwq is ON HOLD Authors: Guo, P., Lam, S.L. Description: Structure of two TTTA repeats Category: Unreleased Structures Category: Guo, P [[C...

New page

'''Unreleased structure'''

The entry 5gwq is ON HOLD

Authors: Guo, P., Lam, S.L.

Description: Structure of two TTTA repeats
[[Category: Unreleased Structures]]
[[Category: Guo, P]]
[[Category: Lam, S.L]]