6u6j - Revision history

OCA at 07:44, 11 October 2023

OCA — Wed, 11 Oct 2023 07:44:53 GMT

←Older revision		Revision as of 07:44, 11 October 2023
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	<StructureSection load='6u6j' size='340' side='right'caption='[[6u6j]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6u6j' size='340' side='right'caption='[[6u6j]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u6j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U6J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6U6J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u6j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U6J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=EQ4:5-O~~-[~~(R)-(2-amino-1H-imidazol-~~1~~-yl)(hydroxy)phosphoryl]guanosine'>EQ4</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]] 1.6Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=LCC:[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCC</scene>, <scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EQ4:5-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]guanosine'>EQ4</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=LCC:[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCC</scene>, <scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</scene></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=6u6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u6j OCA], [~~http~~://pdbe.org/6u6j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6u6j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6u6j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6u6j 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=6u6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u6j OCA], [https://pdbe.org/6u6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u6j RCSB], [https://www.ebi.ac.uk/pdbsum/6u6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u6j 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: Giurgiu, C]]	+	[[Category: Synthetic construct]]
-	[[Category: Szostak~~, J W~~]]	+	[[Category: Giurgiu C]]
-	[[Category: Wright, T]]	+	[[Category: Szostak JW]]
-	[[Category: Zhang, W]]	+	[[Category: Wright T]]
-	~~[[Category: Pyrophosphate]]~~	+	[[Category: Zhang W]]
-	~~[[Category: Rna~~]]	+

OCA at 15:39, 20 November 2019

OCA — Wed, 20 Nov 2019 15:39:45 GMT

←Older revision		Revision as of 15:39, 20 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6u6j is ~~ON HOLD until Paper~~ Publication	+	==RNA-monomer complex containing pyrophosphate linkage==
		+	<StructureSection load='6u6j' size='340' side='right'caption='[[6u6j]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6u6j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U6J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EQ4:5-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]guanosine'>EQ4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=LCC:[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCC</scene>, <scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</scene></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=6u6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u6j OCA], [http://pdbe.org/6u6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u6j RCSB], [http://www.ebi.ac.uk/pdbsum/6u6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u6j ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Achieving multiple cycles of RNA replication within a model protocell would be a critical step toward demonstrating a path from prebiotic chemistry to cellular biology. Any model for early life based on an "RNA world" must account for RNA strand cleavage and hydrolysis, which would degrade primitive genetic information and lead to an accumulation of truncated, phosphate-terminated strands. We show here that cleavage of the phosphodiester backbone is not an end point for RNA replication. Instead, 3'-phosphate-terminated RNA strands can participate in template-directed copying reactions with activated ribonucleotide monomers. These reactions form a pyrophosphate linkage, the stability of which we have characterized in the context of RNA copying chemistry. The presence of free magnesium cations results in cleavage of the pyrophosphate bond within minutes. However, we found that the pyrophosphate bond is relatively stable within an RNA duplex and in the presence of chelated magnesium. We show that, under these conditions, pyrophosphate-linked RNA can act as a template for the polymerization of ribonucleotides into canonical 3'-5' phosphodiester-linked RNA. We suggest that primer extension of 3'-phosphate-terminated RNA followed by template-directed copying represents a plausible nonenzymatic pathway for the salvage and recovery of genetic information following strand cleavage.

-	~~Authors: Zhang~~, W., ~~Szostak~~, J.W.~~, Giurgiu, C~~., ~~Wright, T~~.	+	Prebiotically Plausible "Patching" of RNA Backbone Cleavage through a 3'-5' Pyrophosphate Linkage.,Wright TH, Giurgiu C, Zhang W, Radakovic A, O'Flaherty DK, Zhou L, Szostak JW J Am Chem Soc. 2019 Nov 13;141(45):18104-18112. doi: 10.1021/jacs.9b08237. Epub, 2019 Nov 1. PMID:31651170<ref>PMID:31651170</ref>

-	~~Description: RNA~~-~~monomer complex containing pyrophosphate linkage~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6u6j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Giurgiu, C]]		[[Category: Giurgiu, C]]
-	[[Category: Szostak, J~~.W]]~~	+	[[Category: Szostak, J W]]
-	~~[[Category: Zhang,~~ W]]	+
	[[Category: Wright, T]]		[[Category: Wright, T]]
		+	[[Category: Zhang, W]]
		+	[[Category: Pyrophosphate]]
		+	[[Category: Rna]]

OCA: Protected "6u6j" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2019 08:17:52 GMT

Protected "6u6j" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:17, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6u6j is ON HOLD until Paper Publication Authors: Zhang, W., Szostak, J.W., Giurgiu, C., Wright, T. Description: RNA-monomer complex containing pyro...

OCA — Wed, 02 Oct 2019 08:17:50 GMT

New page: '''Unreleased structure''' The entry 6u6j is ON HOLD until Paper Publication Authors: Zhang, W., Szostak, J.W., Giurgiu, C., Wright, T. Description: RNA-monomer complex containing pyro...

New page

'''Unreleased structure'''

The entry 6u6j is ON HOLD until Paper Publication

Authors: Zhang, W., Szostak, J.W., Giurgiu, C., Wright, T.

Description: RNA-monomer complex containing pyrophosphate linkage
[[Category: Unreleased Structures]]
[[Category: Giurgiu, C]]
[[Category: Szostak, J.W]]
[[Category: Zhang, W]]
[[Category: Wright, T]]