6c8k - Revision history

OCA at 07:30, 1 May 2024

2024-05-01T07:30:18Z

←Older revision		Revision as of 07:30, 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=6c8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c8k OCA], [https://pdbe.org/6c8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c8k RCSB], [https://www.ebi.ac.uk/pdbsum/6c8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c8k 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=6c8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c8k OCA], [https://pdbe.org/6c8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c8k RCSB], [https://www.ebi.ac.uk/pdbsum/6c8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c8k ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5'-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process.
-
-	Crystallographic observation of nonenzymatic RNA primer extension.,Zhang W, Walton T, Li L, Szostak JW Elife. 2018 May 31;7. pii: 36422. doi: 10.7554/eLife.36422. PMID:29851379<ref>PMID:29851379</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6c8k" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:58, 4 October 2023

2023-10-04T14:58:29Z

←Older revision		Revision as of 14:58, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='6c8k' size='340' side='right'caption='[[6c8k]], [[Resolution\|resolution]] 2.26Å' scene=''>		<StructureSection load='6c8k' size='340' side='right'caption='[[6c8k]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c8k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C8K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6C8K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c8k]] 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=6C8K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C8K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EQ1:[2-azanyl-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-1-yl]-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]phosphinic+acid'>EQ1</scene>, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.259Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<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=EQ1:[2-azanyl-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-1-yl]-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]phosphinic+acid'>EQ1</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6c8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c8k OCA], [~~http~~://pdbe.org/6c8k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6c8k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6c8k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6c8k 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=6c8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c8k OCA], [https://pdbe.org/6c8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c8k RCSB], [https://www.ebi.ac.uk/pdbsum/6c8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c8k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Szostak, J W~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Zhang, W~~]]	+	[[Category: Szostak JW]]
-	[[Category: ~~Activated monomer]]~~	+	[[Category: Zhang W]]
-	~~[[Category: Rna~~]]	+

OCA at 17:13, 20 November 2019

2019-11-20T17:13:28Z

←Older revision		Revision as of 17:13, 20 November 2019
Line 1:		Line 1:

	==RNA-activated 2-AIpG monomer complex, 30 min soaking==		==RNA-activated 2-AIpG monomer complex, 30 min soaking==
-	<StructureSection load='6c8k' size='340' side='right' caption='[[6c8k]], [[Resolution\|resolution]] 2.26Å' scene=''>	+	<StructureSection load='6c8k' size='340' side='right'caption='[[6c8k]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6c8k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C8K FirstGlance]. <br>		<table><tr><td colspan='2'>[[6c8k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C8K FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Szostak, J W]]		[[Category: Szostak, J W]]
	[[Category: Zhang, W]]		[[Category: Zhang, W]]
	[[Category: Activated monomer]]		[[Category: Activated monomer]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 07:11, 31 October 2018

2018-10-31T07:11:36Z

←Older revision		Revision as of 07:11, 31 October 2018
Line 8:		Line 8:
	<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=6c8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c8k OCA], [http://pdbe.org/6c8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c8k RCSB], [http://www.ebi.ac.uk/pdbsum/6c8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c8k 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=6c8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c8k OCA], [http://pdbe.org/6c8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c8k RCSB], [http://www.ebi.ac.uk/pdbsum/6c8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c8k ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5'-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process.
		+
		+	Crystallographic observation of nonenzymatic RNA primer extension.,Zhang W, Walton T, Li L, Szostak JW Elife. 2018 May 31;7. pii: 36422. doi: 10.7554/eLife.36422. PMID:29851379<ref>PMID:29851379</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6c8k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:33, 30 May 2018

2018-05-30T05:33:37Z

←Older revision		Revision as of 05:33, 30 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6c8k is ~~ON HOLD until Paper Publication~~	+	==RNA-activated 2-AIpG monomer complex, 30 min soaking==
-		+	<StructureSection load='6c8k' size='340' side='right' caption='[[6c8k]], [[Resolution\|resolution]] 2.26Å' scene=''>
-	~~Authors~~: ~~Zhang~~, W., ~~Szostak~~, J.W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6c8k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C8K FirstGlance]. <br>
-	~~Description~~: ~~RNA~~-~~imidazolium~~-~~bridged intermediate complex~~, ~~4h soaking~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EQ1:[2-azanyl-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]imidazol-1-yl]-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]phosphinic+acid'>EQ1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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>
-	[[Category: Szostak, J.W]]	+	<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=6c8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c8k OCA], [http://pdbe.org/6c8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c8k RCSB], [http://www.ebi.ac.uk/pdbsum/6c8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c8k ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Szostak, J W]]
	[[Category: Zhang, W]]		[[Category: Zhang, W]]
		+	[[Category: Activated monomer]]
		+	[[Category: Rna]]

OCA at 05:08, 7 February 2018

2018-02-07T05:08:50Z

←Older revision		Revision as of 05:08, 7 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6c8k is ON HOLD	+	The entry 6c8k is ON HOLD until Paper Publication

	Authors: Zhang, W., Szostak, J.W.		Authors: Zhang, W., Szostak, J.W.

OCA: Protected "6c8k" [edit=sysop:move=sysop]

2018-01-31T04:51:23Z

Protected "6c8k" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:51, 31 January 2018

OCA: New page: '''Unreleased structure''' The entry 6c8k is ON HOLD Authors: Zhang, W., Szostak, J.W. Description: RNA-imidazolium-bridged intermediate complex, 4h soaking [[Category: Unreleased Stru...

2018-01-31T04:51:22Z

New page: '''Unreleased structure''' The entry 6c8k is ON HOLD Authors: Zhang, W., Szostak, J.W. Description: RNA-imidazolium-bridged intermediate complex, 4h soaking [[Category: Unreleased Stru...

New page

'''Unreleased structure'''

The entry 6c8k is ON HOLD

Authors: Zhang, W., Szostak, J.W.

Description: RNA-imidazolium-bridged intermediate complex, 4h soaking
[[Category: Unreleased Structures]]
[[Category: Szostak, J.W]]
[[Category: Zhang, W]]