4msb - Revision history

OCA at 12:28, 1 March 2024

2024-03-01T12:28:50Z

←Older revision		Revision as of 12:28, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4msb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MSB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4msb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MSB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 1.55Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</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=4msb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4msb OCA], [https://pdbe.org/4msb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4msb RCSB], [https://www.ebi.ac.uk/pdbsum/4msb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4msb 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=4msb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4msb OCA], [https://pdbe.org/4msb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4msb RCSB], [https://www.ebi.ac.uk/pdbsum/4msb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4msb ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity. To better understand the RNA structure and function in the presence of backbone linkage heterogeneity, we obtained high-resolution X-ray crystal structures of a native 10-mer RNA duplex (1.32 A) and two variants: one containing one 2'-5' linkage per strand (1.55 A) and one containing three such linkages per strand (1.20 A). We found that RNA duplexes adjust their local structures to accommodate the perturbation caused by 2'-5' linkages, with the flanking nucleotides buffering the disruptive effects of the isomeric linkage and resulting in a minimally altered global structure. Although most 2'-linked sugars were in the expected 2'-endo conformation, some were partially or fully in the 3'-endo conformation, suggesting that the energy difference between these conformations was relatively small. Our structural and molecular dynamic studies also provide insight into the diminished thermal and chemical stability of the duplex state associated with the presence of 2'-5' linkages. Our results contribute to the view that a low level of 2'-5' substitution would not have been fatal in an early RNA world and may in contrast have been helpful for both the emergence of nonenzymatic RNA replication and the early evolution of functional RNAs.
-
-	Structural insights into the effects of 2'-5' linkages on the RNA duplex.,Sheng J, Li L, Engelhart AE, Gan J, Wang J, Szostak JW Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3050-5. doi:, 10.1073/pnas.1317799111. Epub 2014 Feb 10. PMID:24516151<ref>PMID:24516151</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4msb" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:05, 28 December 2022

2022-12-28T10:05:12Z

←Older revision		Revision as of 10:05, 28 December 2022
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	<StructureSection load='4msb' size='340' side='right'caption='[[4msb]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='4msb' size='340' side='right'caption='[[4msb]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4msb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MSB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4MSB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4msb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MSB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ms9\|4ms9]], [[4msr\|4msr]]~~</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=4msb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4msb OCA], [https://pdbe.org/4msb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4msb RCSB], [https://www.ebi.ac.uk/pdbsum/4msb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4msb 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=4msb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4msb OCA], [~~http~~://pdbe.org/4msb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4msb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4msb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4msb 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: Engelhart~~, A E~~]]	+	[[Category: Engelhart AE]]
-	[[Category: Gan, J]]	+	[[Category: Gan J]]
-	[[Category: Li, L]]	+	[[Category: Li L]]
-	[[Category: Sheng, J]]	+	[[Category: Sheng J]]
-	[[Category: Szostak~~, J W~~]]	+	[[Category: Szostak JW]]
-	[[Category: Wang, J]]	+	[[Category: Wang J]]
-	~~[[Category: 2'-5'-linkage]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 05:10, 13 February 2020

2020-02-13T05:10:32Z

←Older revision		Revision as of 05:10, 13 February 2020
Line 1:		Line 1:

	==RNA 10mer duplex with two 2'-5'-linkages==		==RNA 10mer duplex with two 2'-5'-linkages==
-	<StructureSection load='4msb' size='340' side='right' caption='[[4msb]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='4msb' size='340' side='right'caption='[[4msb]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4msb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MSB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MSB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4msb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MSB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MSB FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Engelhart, A E]]		[[Category: Engelhart, A E]]
	[[Category: Gan, J]]		[[Category: Gan, J]]

OCA at 20:12, 24 January 2018

2018-01-24T20:12:08Z

←Older revision		Revision as of 20:12, 24 January 2018
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: A E~~., Engelhart~~]]	+	[[Category: Engelhart, A E]]
	[[Category: Gan, J]]		[[Category: Gan, J]]
	[[Category: Li, L]]		[[Category: Li, L]]

OCA at 16:11, 11 August 2016

2016-08-11T16:11:24Z

←Older revision		Revision as of 16:11, 11 August 2016
Line 1:		Line 1:
		+
	==RNA 10mer duplex with two 2'-5'-linkages==		==RNA 10mer duplex with two 2'-5'-linkages==
	<StructureSection load='4msb' size='340' side='right' caption='[[4msb]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='4msb' size='340' side='right' caption='[[4msb]], [[Resolution\|resolution]] 1.55Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ms9\|4ms9]], [[4msr\|4msr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ms9\|4ms9]], [[4msr\|4msr]]</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=4msb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4msb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4msb RCSB], [http://www.ebi.ac.uk/pdbsum/4msb 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=4msb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4msb OCA], [http://pdbe.org/4msb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4msb RCSB], [http://www.ebi.ac.uk/pdbsum/4msb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4msb ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4msb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:44, 5 January 2015

2015-01-05T08:44:30Z

←Older revision		Revision as of 08:44, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4msb~~\| ~~PDB~~=4msb \| ~~SCENE~~= }}	+	==RNA 10mer duplex with two 2'-5'-linkages==
-	===RNA ~~10mer~~ duplex ~~with~~ two 2'-5'-linkages~~===~~	+	<StructureSection load='4msb' size='340' side='right' caption='[[4msb]], [[Resolution\|resolution]] 1.55Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24516151}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4msb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MSB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MSB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ms9\|4ms9]], [[4msr\|4msr]]</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=4msb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4msb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4msb RCSB], [http://www.ebi.ac.uk/pdbsum/4msb PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity. To better understand the RNA structure and function in the presence of backbone linkage heterogeneity, we obtained high-resolution X-ray crystal structures of a native 10-mer RNA duplex (1.32 A) and two variants: one containing one 2'-5' linkage per strand (1.55 A) and one containing three such linkages per strand (1.20 A). We found that RNA duplexes adjust their local structures to accommodate the perturbation caused by 2'-5' linkages, with the flanking nucleotides buffering the disruptive effects of the isomeric linkage and resulting in a minimally altered global structure. Although most 2'-linked sugars were in the expected 2'-endo conformation, some were partially or fully in the 3'-endo conformation, suggesting that the energy difference between these conformations was relatively small. Our structural and molecular dynamic studies also provide insight into the diminished thermal and chemical stability of the duplex state associated with the presence of 2'-5' linkages. Our results contribute to the view that a low level of 2'-5' substitution would not have been fatal in an early RNA world and may in contrast have been helpful for both the emergence of nonenzymatic RNA replication and the early evolution of functional RNAs.

-	~~==About this Structure==~~	+	Structural insights into the effects of 2'-5' linkages on the RNA duplex.,Sheng J, Li L, Engelhart AE, Gan J, Wang J, Szostak JW Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3050-5. doi:, 10.1073/pnas.1317799111. Epub 2014 Feb 10. PMID:24516151<ref>PMID:24516151</ref>
-	~~[[4msb]] is a 6 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4MSB OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024516151</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: A E., Engelhart.]]	+	== References ==
-	[[Category: Gan, J.]]	+	<references/>
-	[[Category: Li, L.]]	+	__TOC__
-	[[Category: Sheng, J.]]	+	</StructureSection>
-	[[Category: Szostak, J W.]]	+	[[Category: A E., Engelhart]]
-	[[Category: Wang, J.]]	+	[[Category: Gan, J]]
		+	[[Category: Li, L]]
		+	[[Category: Sheng, J]]
		+	[[Category: Szostak, J W]]
		+	[[Category: Wang, J]]
	[[Category: 2'-5'-linkage]]		[[Category: 2'-5'-linkage]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 09:02, 19 March 2014

2014-03-19T09:02:59Z

←Older revision		Revision as of 09:02, 19 March 2014
Line 1:		Line 1:
	{{STRUCTURE_4msb\| PDB=4msb \| SCENE= }}		{{STRUCTURE_4msb\| PDB=4msb \| SCENE= }}
	===RNA 10mer duplex with two 2'-5'-linkages===		===RNA 10mer duplex with two 2'-5'-linkages===
		+	{{ABSTRACT_PUBMED_24516151}}

	==About this Structure==		==About this Structure==
	[[4msb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MSB OCA].		[[4msb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MSB OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024516151</ref><references group="xtra"/><references/>
	[[Category: A E., Engelhart.]]		[[Category: A E., Engelhart.]]
	[[Category: Gan, J.]]		[[Category: Gan, J.]]

OCA at 05:22, 13 February 2014

2014-02-13T05:22:07Z

←Older revision		Revision as of 05:22, 13 February 2014
Line 1:		Line 1:
-	''~~'Unreleased structure'''~~	+	{{STRUCTURE_4msb\| PDB=4msb \| SCENE= }}
		+	===RNA 10mer duplex with two 2'-5'-linkages===

-	~~The entry~~ 4msb is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4msb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MSB OCA].
-	~~Authors~~: ~~Sheng, J~~.~~, Li, L~~.~~, Engelhart A~~.E., Gan, J., ~~Wang~~, J., Szostak, J.W.	+	[[Category: A E., Engelhart.]]
-		+	[[Category: Gan, J.]]
-	~~Description~~: ~~RNA 10mer duplex with two~~ 2'-5'-~~linkages~~	+	[[Category: Li, L.]]
		+	[[Category: Sheng, J.]]
		+	[[Category: Szostak, J W.]]
		+	[[Category: Wang, J.]]
		+	[[Category: 2'-5'-linkage]]
		+	[[Category: Rna]]

OCA at 09:40, 27 November 2013

2013-11-27T09:40:27Z

←Older revision		Revision as of 09:40, 27 November 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4msb is ON HOLD	+	The entry 4msb is ON HOLD until Paper Publication

	Authors: Sheng, J., Li, L., Engelhart A.E., Gan, J., Wang, J., Szostak, J.W.		Authors: Sheng, J., Li, L., Engelhart A.E., Gan, J., Wang, J., Szostak, J.W.

	Description: RNA 10mer duplex with two 2'-5'-linkages		Description: RNA 10mer duplex with two 2'-5'-linkages

OCA at 07:35, 13 November 2013

2013-11-13T07:35:44Z

←Older revision		Revision as of 07:35, 13 November 2013
Line 3:		Line 3:
	The entry 4msb is ON HOLD		The entry 4msb is ON HOLD

-	Authors: Sheng, J., Li, L., Engelhart A. E., Gan, J., Wang, J., Szostak, J. W.	+	Authors: Sheng, J., Li, L., Engelhart A.E., Gan, J., Wang, J., Szostak, J.W.

	Description: RNA 10mer duplex with two 2'-5'-linkages		Description: RNA 10mer duplex with two 2'-5'-linkages