5uee - Revision history

OCA at 13:26, 4 October 2023

OCA — Wed, 04 Oct 2023 13:26:17 GMT

←Older revision		Revision as of 13:26, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5uee' size='340' side='right'caption='[[5uee]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5uee' size='340' side='right'caption='[[5uee]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uee]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UEE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5UEE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uee]] 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=5UEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UEE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GP3:DIGUANOSINE~~-~~5-TRIPHOSPHATE'>GP3</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]] 1.9Å</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><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GP3:DIGUANOSINE-5-TRIPHOSPHATE'>GP3</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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5ued\|5ued]], [[5uef\|5uef]], [[5ueg\|5ueg]]~~</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=5uee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uee OCA], [https://pdbe.org/5uee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uee RCSB], [https://www.ebi.ac.uk/pdbsum/5uee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uee 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=5uee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uee OCA], [~~http~~://pdbe.org/5uee PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5uee RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5uee PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5uee ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 22:
	</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: ~~Dinucleotide]]~~	+	[[Category: Zhang W]]
-	~~[[Category: Rna~~]]	+

OCA at 12:34, 23 September 2020

OCA — Wed, 23 Sep 2020 12:34:01 GMT

←Older revision		Revision as of 12:34, 23 September 2020
Line 1:		Line 1:

	==RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G==		==RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G==
-	<StructureSection load='5uee' size='340' side='right' caption='[[5uee]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5uee' size='340' side='right'caption='[[5uee]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uee]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UEE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UEE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uee]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UEE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5UEE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GP3:DIGUANOSINE-5-TRIPHOSPHATE'>GP3</scene>, <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=GP3:DIGUANOSINE-5-TRIPHOSPHATE'>GP3</scene>, <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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ued\|5ued]], [[5uef\|5uef]], [[5ueg\|5ueg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ued\|5ued]], [[5uef\|5uef]], [[5ueg\|5ueg]]</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=5uee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uee OCA], [http://pdbe.org/5uee PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uee RCSB], [http://www.ebi.ac.uk/pdbsum/5uee PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uee 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=5uee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uee OCA], [http://pdbe.org/5uee PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uee RCSB], [http://www.ebi.ac.uk/pdbsum/5uee PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uee ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Szostak, J W]]		[[Category: Szostak, J W]]
	[[Category: Tam, C P]]		[[Category: Tam, C P]]

OCA at 03:52, 4 August 2017

OCA — Fri, 04 Aug 2017 03:52:33 GMT

←Older revision		Revision as of 03:52, 4 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5uee is ~~ON HOLD until Jan 01 2019~~	+	==RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G==
		+	<StructureSection load='5uee' size='340' side='right' caption='[[5uee]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5uee]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UEE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UEE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GP3:DIGUANOSINE-5-TRIPHOSPHATE'>GP3</scene>, <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></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ued\|5ued]], [[5uef\|5uef]], [[5ueg\|5ueg]]</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=5uee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uee OCA], [http://pdbe.org/5uee PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uee RCSB], [http://www.ebi.ac.uk/pdbsum/5uee PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uee ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The nonenzymatic copying of RNA templates with imidazole-activated nucleotides is a well-studied model for the emergence of RNA self-replication during the origin of life. We have recently discovered that this reaction can proceed through the formation of an imidazolium-bridged dinucleotide intermediate that reacts rapidly with the primer. To gain insight into the relationship between the structure of this intermediate and its reactivity, we cocrystallized an RNA primer-template complex with a close analog of the intermediate, the triphosphate-bridged guanosine dinucleotide GpppG, and solved a high-resolution X-ray structure of the complex. The structure shows that GpppG binds the RNA template through two Watson-Crick base pairs, with the primer 3'-hydroxyl oriented to attack the 5'-phosphate of the adjacent G residue. Thus, the GpppG structure suggests that the bound imidazolium-bridged dinucleotide intermediate would be preorganized to react with the primer by in-line SN2 substitution. The structures of bound GppG and GppppG suggest that the length and flexibility of the 5'-5' linkage are important for optimal preorganization of the complex, whereas the position of the 5'-phosphate of bound pGpG explains the slow rate of oligonucleotide ligation reactions. Our studies provide a structural interpretation for the observed reactivity of the imidazolium-bridged dinucleotide intermediate in nonenzymatic RNA primer extension.

-	~~Authors: Zhang~~, W., Tam, C.P., ~~Szostak, J~~.W.	+	Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex.,Zhang W, Tam CP, Walton T, Fahrenbach AC, Birrane G, Szostak JW Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):7659-7664. doi:, 10.1073/pnas.1704006114. Epub 2017 Jul 3. PMID:28673998<ref>PMID:28673998</ref>

-	~~Description: RNA primer~~-~~template complex with guanosine dinucleotide ligand G(5')ppp(5')G~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Szostak~~, ~~J.W~~]]	+	<div class="pdbe-citations 5uee" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Szostak, J W]]
		+	[[Category: Tam, C P]]
	[[Category: Zhang, W]]		[[Category: Zhang, W]]
-	[[Category: ~~Tam, C.P~~]]	+	[[Category: Dinucleotide]]
		+	[[Category: Rna]]

OCA at 18:58, 15 March 2017

OCA — Wed, 15 Mar 2017 18:58:48 GMT

←Older revision		Revision as of 18:58, 15 March 2017
Line 7:		Line 7:
	Description: RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G		Description: RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Zhang, W]]
	[[Category: Szostak, J.W]]		[[Category: Szostak, J.W]]
		+	[[Category: Zhang, W]]
	[[Category: Tam, C.P]]		[[Category: Tam, C.P]]

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

OCA — Wed, 18 Jan 2017 14:45:19 GMT

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

←Older revision

Revision as of 14:45, 18 January 2017

OCA: New page: '''Unreleased structure''' The entry 5uee is ON HOLD until Jan 01 2019 Authors: Zhang, W., Tam, C.P., Szostak, J.W. Description: RNA primer-template complex with guanosine dinucleotide...

OCA — Wed, 18 Jan 2017 14:45:18 GMT

New page: '''Unreleased structure''' The entry 5uee is ON HOLD until Jan 01 2019 Authors: Zhang, W., Tam, C.P., Szostak, J.W. Description: RNA primer-template complex with guanosine dinucleotide...

New page

'''Unreleased structure'''

The entry 5uee is ON HOLD until Jan 01 2019

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

Description: RNA primer-template complex with guanosine dinucleotide ligand G(5')ppp(5')G
[[Category: Unreleased Structures]]
[[Category: Zhang, W]]
[[Category: Szostak, J.W]]
[[Category: Tam, C.P]]