5l00 - Revision history

OCA at 12:46, 4 October 2023

2023-10-04T12:46:05Z

←Older revision		Revision as of 12:46, 4 October 2023
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	<StructureSection load='5l00' size='340' side='right'caption='[[5l00]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='5l00' size='340' side='right'caption='[[5l00]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l00]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L00 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5L00 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l00]] is a 4 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=5L00 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5L00 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 1.25Å</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=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~~://proteopedia.org/fgij/fg.htm?mol=5l00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l00 OCA], [~~http~~://pdbe.org/5l00 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5l00 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5l00 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5l00 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=5l00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l00 OCA], [https://pdbe.org/5l00 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5l00 RCSB], [https://www.ebi.ac.uk/pdbsum/5l00 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5l00 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: ~~Szostak, J W~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Tam, C P~~]]	+	[[Category: Szostak JW]]
-	[[Category: ~~Zhang, W~~]]	+	[[Category: Tam CP]]
-	[[Category: ~~Rna~~]]	+	[[Category: Zhang W]]

OCA at 06:38, 5 August 2020

2020-08-05T06:38:14Z

←Older revision		Revision as of 06:38, 5 August 2020
Line 1:		Line 1:

	==Self-complimentary RNA 15mer binding with GMP monomers==		==Self-complimentary RNA 15mer binding with GMP monomers==
-	<StructureSection load='5l00' size='340' side='right' caption='[[5l00]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='5l00' size='340' side='right'caption='[[5l00]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l00]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L00 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5L00 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l00]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L00 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5L00 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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='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='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=5l00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l00 OCA], [http://pdbe.org/5l00 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l00 RCSB], [http://www.ebi.ac.uk/pdbsum/5l00 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l00 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=5l00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l00 OCA], [http://pdbe.org/5l00 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l00 RCSB], [http://www.ebi.ac.uk/pdbsum/5l00 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l00 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Szostak, J W]]		[[Category: Szostak, J W]]
	[[Category: Tam, C P]]		[[Category: Tam, C P]]
	[[Category: Zhang, W]]		[[Category: Zhang, W]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 08:10, 18 January 2017

2017-01-18T08:10:25Z

←Older revision		Revision as of 08:10, 18 January 2017
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	<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=5l00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l00 OCA], [http://pdbe.org/5l00 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l00 RCSB], [http://www.ebi.ac.uk/pdbsum/5l00 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l00 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=5l00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l00 OCA], [http://pdbe.org/5l00 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l00 RCSB], [http://www.ebi.ac.uk/pdbsum/5l00 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l00 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many high-resolution crystal structures have contributed to our understanding of the reaction pathway for catalysis by DNA and RNA polymerases, but the structural basis of nonenzymatic template-directed RNA replication has not been studied in comparable detail. Here we present crystallographic studies of the binding of ribonucleotide monomers to RNA primer-template complexes, with the goal of improving our understanding of the mechanism of nonenzymatic RNA copying, and of catalysis by polymerases. To explore how activated ribonucleotides recognize and bind to RNA templates, we synthesized an unreactive phosphonate-linked pyrazole analogue of guanosine 5'-phosphoro-2-methylimidazolide (2-MeImpG), a highly activated nucleotide that has been used extensively to study nonenzymatic primer extension. We cocrystallized this analogue with structurally rigidified RNA primer-template complexes carrying single or multiple monomer binding sites, and obtained high-resolution X-ray structures of these complexes. In addition to Watson-Crick base pairing, we repeatedly observed noncanonical guanine:cytidine base pairs in our crystal structures. In most structures, the phosphate and leaving group moieties of the monomers were highly disordered, while in others the distance from O3' of the primer to the phosphorus of the incoming monomer was too great to allow for reaction. We suggest that these effects significantly influence the rate and fidelity of nonenzymatic RNA replication, and that even primitive ribozyme polymerases could enhance RNA replication by enforcing Watson-Crick base pairing between monomers and primer-template complexes, and by bringing the reactive functional groups into closer proximity.
		+
		+	Unusual Base-Pairing Interactions in Monomer-Template Complexes.,Zhang W, Tam CP, Wang J, Szostak JW ACS Cent Sci. 2016 Dec 28;2(12):916-926. doi: 10.1021/acscentsci.6b00278. Epub, 2016 Nov 2. PMID:28058281<ref>PMID:28058281</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5l00" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 02:16, 11 December 2016

2016-12-11T02:16:21Z

←Older revision		Revision as of 02:16, 11 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5l00 is ~~ON HOLD until Paper Publication~~	+	==Self-complimentary RNA 15mer binding with GMP monomers==
-		+	<StructureSection load='5l00' size='340' side='right' caption='[[5l00]], [[Resolution\|resolution]] 1.25Å' scene=''>
-	~~Authors~~: ~~Zhang~~, W., ~~Tam~~, C.P., ~~Szostak~~, J.W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5l00]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L00 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5L00 FirstGlance]. <br>
-	~~Description~~: ~~Self-complimentary RNA 15mer binding with GMP monomers~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>
		+	<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=5l00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l00 OCA], [http://pdbe.org/5l00 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l00 RCSB], [http://www.ebi.ac.uk/pdbsum/5l00 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l00 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Szostak, J W]]
		+	[[Category: Tam, C P]]
	[[Category: Zhang, W]]		[[Category: Zhang, W]]
-	[[Category: ~~Szostak, J.W]]~~	+	[[Category: Rna]]
-	~~[[Category: Tam, C.P~~]]	+

OCA at 14:29, 9 September 2016

2016-09-09T14:29:03Z

←Older revision		Revision as of 14:29, 9 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5l00 is ON HOLD	+	The entry 5l00 is ON HOLD until Paper Publication

	Authors: Zhang, W., Tam, C.P., Szostak, J.W.		Authors: Zhang, W., Tam, C.P., Szostak, J.W.

OCA: Protected "5l00" [edit=sysop:move=sysop]

2016-08-04T02:18:18Z

Protected "5l00" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:18, 4 August 2016

OCA: New page: '''Unreleased structure''' The entry 5l00 is ON HOLD Authors: Zhang, W., Tam, C.P., Szostak, J.W. Description: Self-complimentary RNA 15mer binding with GMP monomers [[Category: Unrele...

2016-08-04T02:18:16Z

New page: '''Unreleased structure''' The entry 5l00 is ON HOLD Authors: Zhang, W., Tam, C.P., Szostak, J.W. Description: Self-complimentary RNA 15mer binding with GMP monomers [[Category: Unrele...

New page

'''Unreleased structure'''

The entry 5l00 is ON HOLD

Authors: Zhang, W., Tam, C.P., Szostak, J.W.

Description: Self-complimentary RNA 15mer binding with GMP monomers
[[Category: Unreleased Structures]]
[[Category: Zhang, W]]
[[Category: Szostak, J.W]]
[[Category: Tam, C.P]]