4e6b - Revision history

OCA at 11:02, 1 March 2024

2024-03-01T11:02:09Z

← Older revision		Revision as of 11:02, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e6b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E6B FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e6b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E6B 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=4e6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e6b OCA], [https://pdbe.org/4e6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e6b RCSB], [https://www.ebi.ac.uk/pdbsum/4e6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e6b ProSAT]</span></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]] 1.47Å</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=4e6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e6b OCA], [https://pdbe.org/4e6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e6b RCSB], [https://www.ebi.ac.uk/pdbsum/4e6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e6b ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Human genetic trinucleotide repeat expansion diseases (TREDs) are characterized by triplet repeat expansions, most frequently found as CNG-tracts in genome. At RNA level, such expansions suggestively result in formation of double-helical hairpins that become a potential source for small RNAs involved in RNA interference (RNAi). Here, we present three crystal structures of RNA fragments composed of triplet repeats CUG and CGG/CUG, as well as two crystal structures of same triplets in a protein-bound state. We show that both 20mer pG(CUG)(6)C and 19mer pGG(CGG)(3)(CUG)(2)CC form A-RNA duplexes, in which U.U or G.U mismatches are flanked/stabilized by two consecutive Watson-Crick G.C base pairs resulting in high-stacking GpC steps in every third position of the duplex. Despite interruption of this regularity in another 19mer, p(CGG)(3)C(CUG)(3), the oligonucleotide still forms regular double-helical structure, characterized, however, by 12 bp (rather than 11 bp) per turn. Analysis of newly determined molecular structures reveals the dynamic aspects of U.U and G.U mismatching within CNG-repetitive A-RNA and in a protein-bound state, as well as identifies an additional mode of U.U pairing essential for its dynamics and sheds the light on possible role of regularity of trinucleotide repeats for double-helical RNA structure. Findings are important for understanding the structural behavior of CNG-repetitive RNA double helices implicated in TREDs.

	~~Structural dynamics of double-helical RNAs composed of CUG/CUG- and CUG/CGG-repeats.,Tamjar J, Katorcha E, Popov A, Malinina L J Biomol Struct Dyn. 2012 Jun 25. PMID:22731704<ref>PMID:22731704</ref>~~

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4e6b" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:53, 28 September 2022

2022-09-28T06:53:16Z

← Older revision		Revision as of 06:53, 28 September 2022
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	<StructureSection load='4e6b' size='340' side='right'caption='[[4e6b]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='4e6b' size='340' side='right'caption='[[4e6b]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e6b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E6B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E6B FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e6b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E6B FirstGlance]. <br>
	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e48\|4e48]], [[4e5c\|4e5c]]</td></tr>~~		</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=4e6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e6b OCA], [https://pdbe.org/4e6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e6b RCSB], [https://www.ebi.ac.uk/pdbsum/4e6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e6b ProSAT]</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=4e6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e6b OCA], [~~http~~://pdbe.org/4e6b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e6b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e6b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e6b 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: Malinina, L]]		[[Category: Malinina L]]
	[[Category: Popov, A]]		[[Category: Popov A]]
	[[Category: Tamjar, J]]		[[Category: Tamjar J]]
	~~[[Category: Rna]]~~
	~~[[Category: Sirna]]~~
	~~[[Category: Trinucleotide repeat expansion~~]]

OCA at 16:31, 28 August 2019

2019-08-28T16:31:41Z

← Older revision		Revision as of 16:31, 28 August 2019
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	==Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3==		==Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3==
	<StructureSection load='4e6b' size='340' side='right' caption='[[4e6b]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='4e6b' size='340' side='right'caption='[[4e6b]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e6b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E6B FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e6b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E6B FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Malinina, L]]		[[Category: Malinina, L]]
	[[Category: Popov, A]]		[[Category: Popov, A]]

OCA at 12:43, 11 August 2016

2016-08-11T12:43:36Z

← Older revision		Revision as of 12:43, 11 August 2016
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	==Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3==		==Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3==
	<StructureSection load='4e6b' size='340' side='right' caption='[[4e6b]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='4e6b' size='340' side='right' caption='[[4e6b]], [[Resolution\|resolution]] 1.47Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4e6b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E6B FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e6b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E6B FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e48\|4e48]], [[4e5c\|4e5c]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e48\|4e48]], [[4e5c\|4e5c]]</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=4e6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e6b RCSB], [http://www.ebi.ac.uk/pdbsum/4e6b 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=4e6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e6b OCA], [http://pdbe.org/4e6b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e6b RCSB], [http://www.ebi.ac.uk/pdbsum/4e6b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e6b ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4e6b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:45, 4 January 2015

2015-01-04T12:45:29Z

← Older revision		Revision as of 12:45, 4 January 2015
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	[[~~Image~~:~~4e6b~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3==
			<StructureSection load='4e6b' size='340' side='right' caption='[[4e6b]], [[Resolution\|resolution]] 1.47Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e6b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E6B FirstGlance]. <br>
			</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e48\|4e48]], [[4e5c\|4e5c]]</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=4e6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e6b RCSB], [http://www.ebi.ac.uk/pdbsum/4e6b PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Human genetic trinucleotide repeat expansion diseases (TREDs) are characterized by triplet repeat expansions, most frequently found as CNG-tracts in genome. At RNA level, such expansions suggestively result in formation of double-helical hairpins that become a potential source for small RNAs involved in RNA interference (RNAi). Here, we present three crystal structures of RNA fragments composed of triplet repeats CUG and CGG/CUG, as well as two crystal structures of same triplets in a protein-bound state. We show that both 20mer pG(CUG)(6)C and 19mer pGG(CGG)(3)(CUG)(2)CC form A-RNA duplexes, in which U.U or G.U mismatches are flanked/stabilized by two consecutive Watson-Crick G.C base pairs resulting in high-stacking GpC steps in every third position of the duplex. Despite interruption of this regularity in another 19mer, p(CGG)(3)C(CUG)(3), the oligonucleotide still forms regular double-helical structure, characterized, however, by 12 bp (rather than 11 bp) per turn. Analysis of newly determined molecular structures reveals the dynamic aspects of U.U and G.U mismatching within CNG-repetitive A-RNA and in a protein-bound state, as well as identifies an additional mode of U.U pairing essential for its dynamics and sheds the light on possible role of regularity of trinucleotide repeats for double-helical RNA structure. Findings are important for understanding the structural behavior of CNG-repetitive RNA double helices implicated in TREDs.

	~~{{STRUCTURE_4e6b\| PDB=4e6b \| SCENE= }}~~		Structural dynamics of double-helical RNAs composed of CUG/CUG- and CUG/CGG-repeats.,Tamjar J, Katorcha E, Popov A, Malinina L J Biomol Struct Dyn. 2012 Jun 25. PMID:22731704<ref>PMID:22731704</ref>

	~~===Crystal Structure~~ of ~~statistically disordered 19mer duplex p(CGG)3C(CUG)3===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_22731704}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[4e6b]] is a 4 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4E6B OCA].~~		</StructureSection>
			[[Category: Malinina, L]]
	==~~Reference~~==		[[Category: Popov, A]]
	<~~ref group="xtra">PMID:022731704<~~/~~ref~~><~~references group="xtra"~~/>		[[Category: Tamjar, J]]
	[[Category: Malinina, L.]]
	[[Category: Popov, A.]]
	[[Category: Tamjar, J.]]
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Sirna]]		[[Category: Sirna]]
	[[Category: Trinucleotide repeat expansion]]		[[Category: Trinucleotide repeat expansion]]

OCA at 05:38, 29 August 2012

2012-08-29T05:38:01Z

← Older revision		Revision as of 05:38, 29 August 2012
Line 1:		Line 1:
	[[Image:4e6b.~~jpg~~\|left\|200px]]		[[Image:4e6b.png\|left\|200px]]

	{{STRUCTURE_4e6b\| PDB=4e6b \| SCENE= }}		{{STRUCTURE_4e6b\| PDB=4e6b \| SCENE= }}

OCA at 08:13, 11 July 2012

2012-07-11T08:13:24Z

← Older revision		Revision as of 08:13, 11 July 2012
Line 1:		Line 1:
	~~'''Unreleased structure'''~~		[[Image:4e6b.jpg\|left\|200px]]

	~~The entry~~ 4e6b ~~is ON HOLD~~ ~~until Paper Publication~~		{{STRUCTURE_4e6b\| PDB=4e6b \| SCENE= }}

	~~Authors: Malinina, L., Popov, A., Tamjar, J.~~		===Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3===

	~~Description~~: ~~Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3~~		{{ABSTRACT_PUBMED_22731704}}

			==About this Structure==
			[[4e6b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E6B OCA].

			==Reference==
			<ref group="xtra">PMID:022731704</ref><references group="xtra"/>
			[[Category: Malinina, L.]]
			[[Category: Popov, A.]]
			[[Category: Tamjar, J.]]
			[[Category: Rna]]
			[[Category: Sirna]]
			[[Category: Trinucleotide repeat expansion]]

OCA at 06:39, 11 April 2012

2012-04-11T06:39:05Z

← Older revision		Revision as of 06:39, 11 April 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e6b is ON HOLD		The entry 4e6b is ON HOLD until Paper Publication

	Authors: Malinina, L., Popov, A., Tamjar, J.		Authors: Malinina, L., Popov, A., Tamjar, J.

	Description: Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3		Description: Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3

OCA: Protected "4e6b" [edit=sysop:move=sysop]

2012-03-21T07:18:51Z

Protected "4e6b" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:18, 21 March 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4e6b is ON HOLD Authors: Malinina, L., Popov, A., Tamjar, J. Description: Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3

2012-03-21T07:18:50Z

New page: '''Unreleased structure''' The entry 4e6b is ON HOLD Authors: Malinina, L., Popov, A., Tamjar, J. Description: Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3

New page

'''Unreleased structure'''

The entry 4e6b is ON HOLD

Authors: Malinina, L., Popov, A., Tamjar, J.

Description: Crystal Structure of statistically disordered 19mer duplex p(CGG)3C(CUG)3