6bmd - Revision history

OCA at 14:45, 4 October 2023

2023-10-04T14:45:40Z

← Older revision		Revision as of 14:45, 4 October 2023
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	<StructureSection load='6bmd' size='340' side='right'caption='[[6bmd]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6bmd' size='340' side='right'caption='[[6bmd]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bmd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BMD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6BMD FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bmd]] is a 6 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=6BMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BMD FirstGlance]. <br>
	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><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></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]] 3Å</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=6bmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmd OCA], [~~http~~://pdbe.org/6bmd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bmd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bmd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmd ProSAT]</span></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></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=6bmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmd OCA], [https://pdbe.org/6bmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bmd RCSB], [https://www.ebi.ac.uk/pdbsum/6bmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmd 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: ~~Zhang, W~~]]		[[Category: Szostak JW]]
	[[Category: ~~Gpppg]]~~		[[Category: Zhang W]]
	~~[[Category: Helper]]~~
	~~[[Category: Intermediate]]~~
	~~[[Category: Rna~~]]

OCA at 08:50, 11 November 2020

2020-11-11T08:50:51Z

← Older revision		Revision as of 08:50, 11 November 2020
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	==RNA hairpin containing GpppG-oligo to mimic intermediate formed by activated monomer and activated downstream helper==		==RNA hairpin containing GpppG-oligo to mimic intermediate formed by activated monomer and activated downstream helper==
	<StructureSection load='6bmd' size='340' side='right' caption='[[6bmd]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6bmd' size='340' side='right'caption='[[6bmd]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6bmd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BMD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BMD FirstGlance]. <br>		<table><tr><td colspan='2'>[[6bmd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BMD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6BMD FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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></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=6bmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmd OCA], [http://pdbe.org/6bmd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bmd RCSB], [http://www.ebi.ac.uk/pdbsum/6bmd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmd 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=6bmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmd OCA], [http://pdbe.org/6bmd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bmd RCSB], [http://www.ebi.ac.uk/pdbsum/6bmd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmd 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: Zhang, W]]		[[Category: Zhang, W]]

OCA at 07:28, 22 February 2018

2018-02-22T07:28:21Z

← Older revision		Revision as of 07:28, 22 February 2018
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	~~'''Unreleased structure'''~~

	~~The entry~~ 6bmd is ~~ON HOLD until Paper~~ Publication		==RNA hairpin containing GpppG-oligo to mimic intermediate formed by activated monomer and activated downstream helper==
			<StructureSection load='6bmd' size='340' side='right' caption='[[6bmd]], [[Resolution\|resolution]] 3.00Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[6bmd]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BMD FirstGlance]. <br>
			</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><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></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=6bmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bmd OCA], [http://pdbe.org/6bmd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bmd RCSB], [http://www.ebi.ac.uk/pdbsum/6bmd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bmd ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Nonenzymatic RNA primer extension by activated mononucleotides has long served as a model for the study of prebiotic RNA copying. We have recently shown that the rate of primer extension is greatly enhanced by the formation of an imidazolium-bridged dinucleotide between the incoming monomer and a second, downstream activated monomer. However, the rate of primer extension is further enhanced if the downstream monomer is replaced by an activated oligonucleotide. Even an unactivated downstream oligonucleotide provides a modest enhancement in the rate of reaction of a primer with a single activated monomer. Here we study the mechanism of these effects through crystallographic studies of RNA complexes with the recently synthesized nonhydrolyzable substrate analog, guanosine 5'-(4-methylimidazolyl)-phosphonate (ICG). ICG mimics 2-methylimidazole activated guanosine-5'-phosphate (2-MeImpG), a commonly used substrate in nonenzymatic primer extension experiments. We present crystal structures of primer-template complexes with either one or two ICG residues bound downstream of a primer. In both cases, the aryl-phosphonate moiety of the ICG adjacent to the primer is disordered. To investigate the effect of a downstream oligonucleotide, we transcribed a short RNA oligonucleotide with either a 5'-ICG residue, a 5'-phosphate or a 5'-hydroxyl. We then determined crystal structures of primer-template complexes with a bound ICG monomer sandwiched between the primer and each of the three downstream oligonucleotides. Surprisingly, all three oligonucleotides rigidify the ICG monomer conformation and position it for attack by the primer 3'-hydroxyl. Furthermore, when GpppG, an analog of the imidazolium-bridged intermediate, is sandwiched between an upstream primer and a downstream helper oligonucleotide, or covalently linked to the 5'-end of the downstream oligonucleotide, the complex is better preorganized for primer extension than in the absence of a downstream oligonucleotide. Our results suggest that a downstream helper oligonucleotide contributes to the catalysis of primer extension by favoring a reactive conformation of the primer-template-intermediate complex.

	~~Authors:~~ Zhang, W., Szostak, J.W.		Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.,Zhang W, Tam CP, Zhou L, Oh SS, Wang J, Szostak JW J Am Chem Soc. 2018 Feb 13. doi: 10.1021/jacs.7b11750. PMID:29411978<ref>PMID:29411978</ref>

	~~Description~~: ~~RNA hairpin containing GpppG-oligo to mimic intermediate formed by activated monomer and activated downstream helper~~		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 6bmd" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Szostak, J W]]
	[[Category: Zhang, W]]		[[Category: Zhang, W]]
			[[Category: Gpppg]]
			[[Category: Helper]]
			[[Category: Intermediate]]
			[[Category: Rna]]

OCA at 05:04, 29 November 2017

2017-11-29T05:04:19Z

← Older revision		Revision as of 05:04, 29 November 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6bmd is ON HOLD		The entry 6bmd is ON HOLD until Paper Publication

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

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

2017-11-22T06:36:19Z

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

← Older revision	Revision as of 06:36, 22 November 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6bmd is ON HOLD Authors: Zhang, W., Szostak, J.W. Description: RNA hairpin containing GpppG-oligo to mimic intermediate formed by activated monomer...

2017-11-22T06:36:18Z

New page: '''Unreleased structure''' The entry 6bmd is ON HOLD Authors: Zhang, W., Szostak, J.W. Description: RNA hairpin containing GpppG-oligo to mimic intermediate formed by activated monomer...

New page

'''Unreleased structure'''

The entry 6bmd is ON HOLD

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

Description: RNA hairpin containing GpppG-oligo to mimic intermediate formed by activated monomer and activated downstream helper
[[Category: Unreleased Structures]]
[[Category: Szostak, J.W]]
[[Category: Zhang, W]]