6d8a - Revision history

OCA at 14:33, 13 March 2024

2024-03-13T14:33:08Z

← Older revision		Revision as of 14:33, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6d8a' size='340' side='right'caption='[[6d8a]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6d8a' size='340' side='right'caption='[[6d8a]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6d8a]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D8A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6D8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[6d8a]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides_ATCC_17025 Cereibacter sphaeroides ATCC 17025]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D8A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 2.251Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6d8p\|6d8p]], [[6d8f\|6d8f]], [[6d95\|6d95]], [[6d92\|6d92]]~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=6d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d8a OCA], [~~http~~://pdbe.org/6d8a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6d8a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6d8a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6d8a 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=6d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d8a OCA], [https://pdbe.org/6d8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d8a RCSB], [https://www.ebi.ac.uk/pdbsum/6d8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d8a ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style~~=~~"background-color:#fffaf0;">~~		== Function ==
	== ~~Publication Abstract from PubMed~~ ==		[https://www.uniprot.org/uniprot/A4WYU7_CERS5 A4WYU7_CERS5]
	Prokaryotic Argonaute (Ago) proteins were recently shown to target foreign genetic elements, thus making them a perfect model for studies of interference mechanisms. Here, we study interactions of Rhodobacter sphaeroides Ago (RsAgo) with guide RNA (gRNA) and fully complementary or imperfect target DNA (tDNA) using biochemical and structural approaches. We show that RsAgo can specifically recognize both the first nucleotide in gRNA and complementary nucleotide in tDNA, and both interactions contribute to nucleic acid binding. Non-canonical pairs and bulges on the target strand can be accommodated by RsAgo with minimal perturbation of the duplex but significantly reduce RsAgo affinity to tDNA. Surprisingly, mismatches between gRNA and tDNA induce dissociation of the guide-target duplex from RsAgo. Our results reveal plasticity in the ability of Ago proteins to accommodate helical imperfections, show how this might affect the efficiency of RNA silencing, and suggest a potential mechanism for guide release and Ago recycling.

	Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.,Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ Cell Rep. 2018 Jul 10;24(2):453-462. doi: ~~10.1016~~/~~j.celrep.2018.06.021. PMID:29996105<ref>PMID:29996105</ref>~~

	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~
	</~~div>~~
	~~<div class="pdbe-citations 6d8a" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references~~/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Cereibacter sphaeroides ATCC 17025]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Esyunina, D]]		[[Category: Esyunina D]]
	[[Category: Liu, Y]]		[[Category: Liu Y]]
	[[Category: Olovnikov, I]]		[[Category: Olovnikov I]]
	[[Category: Patel~~, D J~~]]		[[Category: Patel DJ]]
	[[Category: Teplova, M]]		[[Category: Teplova M]]
	~~[[Category: Guide rna]]~~
	~~[[Category: Non-canonical base pairs and bulge]]~~
	~~[[Category: Rna binding protein]]~~
	~~[[Category: Rna-dna heteroduplex]]~~
	~~[[Category: Target dna~~]]

OCA at 09:04, 11 November 2020

2020-11-11T09:04:09Z

← Older revision		Revision as of 09:04, 11 November 2020
Line 1:		Line 1:

	==RsAgo Ternary Complex with guide RNA and Target DNA Containing A-A Bulge Within the Seed Segment of the Target Strand==		==RsAgo Ternary Complex with guide RNA and Target DNA Containing A-A Bulge Within the Seed Segment of the Target Strand==
	<StructureSection load='6d8a' size='340' side='right' caption='[[6d8a]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6d8a' size='340' side='right'caption='[[6d8a]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6d8a]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D8A OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6D8A FirstGlance]. <br>		<table><tr><td colspan='2'>[[6d8a]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D8A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6D8A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6d8p\|6d8p]], [[6d8f\|6d8f]], [[6d95\|6d95]], [[6d92\|6d92]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6d8p\|6d8p]], [[6d8f\|6d8f]], [[6d95\|6d95]], [[6d92\|6d92]]</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=6d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d8a OCA], [http://pdbe.org/6d8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d8a RCSB], [http://www.ebi.ac.uk/pdbsum/6d8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d8a 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=6d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d8a OCA], [http://pdbe.org/6d8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d8a RCSB], [http://www.ebi.ac.uk/pdbsum/6d8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d8a 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: Esyunina, D]]		[[Category: Esyunina, D]]
	[[Category: Liu, Y]]		[[Category: Liu, Y]]

OCA at 07:19, 25 July 2018

2018-07-25T07:19:05Z

← Older revision		Revision as of 07:19, 25 July 2018
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6d8a is ~~ON HOLD~~		==RsAgo Ternary Complex with guide RNA and Target DNA Containing A-A Bulge Within the Seed Segment of the Target Strand==
			<StructureSection load='6d8a' size='340' side='right' caption='[[6d8a]], [[Resolution\|resolution]] 2.25Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[6d8a]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D8A FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6d8p\|6d8p]], [[6d8f\|6d8f]], [[6d95\|6d95]], [[6d92\|6d92]]</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=6d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d8a OCA], [http://pdbe.org/6d8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d8a RCSB], [http://www.ebi.ac.uk/pdbsum/6d8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d8a ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Prokaryotic Argonaute (Ago) proteins were recently shown to target foreign genetic elements, thus making them a perfect model for studies of interference mechanisms. Here, we study interactions of Rhodobacter sphaeroides Ago (RsAgo) with guide RNA (gRNA) and fully complementary or imperfect target DNA (tDNA) using biochemical and structural approaches. We show that RsAgo can specifically recognize both the first nucleotide in gRNA and complementary nucleotide in tDNA, and both interactions contribute to nucleic acid binding. Non-canonical pairs and bulges on the target strand can be accommodated by RsAgo with minimal perturbation of the duplex but significantly reduce RsAgo affinity to tDNA. Surprisingly, mismatches between gRNA and tDNA induce dissociation of the guide-target duplex from RsAgo. Our results reveal plasticity in the ability of Ago proteins to accommodate helical imperfections, show how this might affect the efficiency of RNA silencing, and suggest a potential mechanism for guide release and Ago recycling.

	~~Authors:~~ Liu, Y., Esyunina, D., Olovnikov, I., Teplova, M., Patel~~, D~~.J.		Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.,Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ Cell Rep. 2018 Jul 10;24(2):453-462. doi: 10.1016/j.celrep.2018.06.021. PMID:29996105<ref>PMID:29996105</ref>

	~~Description: RsAgo Ternary Complexes Containing A-A Bulge Within~~ the ~~Seed Segment~~ of ~~the Target Strand~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[Category~~: ~~Unreleased Structures]]~~		</div>
			<div class="pdbe-citations 6d8a" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
	[[Category: Esyunina, D]]		[[Category: Esyunina, D]]
	[[Category: Patel, D.J]]		[[Category: Liu, Y]]
			[[Category: Olovnikov, I]]
			[[Category: Patel, D J]]
	[[Category: Teplova, M]]		[[Category: Teplova, M]]
	[[Category: ~~Olovnikov, I~~]]		[[Category: Guide rna]]
	[[Category: ~~Liu, Y~~]]		[[Category: Non-canonical base pairs and bulge]]
			[[Category: Rna binding protein]]
			[[Category: Rna-dna heteroduplex]]
			[[Category: Target dna]]

OCA: Protected "6d8a" [edit=sysop:move=sysop]

2018-05-02T06:49:21Z

Protected "6d8a" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:49, 2 May 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6d8a is ON HOLD Authors: Liu, Y., Esyunina, D., Olovnikov, I., Teplova, M., Patel, D.J. Description: RsAgo Ternary Complexes Containing A-A Bulge W...

2018-05-02T06:49:19Z

New page: '''Unreleased structure''' The entry 6d8a is ON HOLD Authors: Liu, Y., Esyunina, D., Olovnikov, I., Teplova, M., Patel, D.J. Description: RsAgo Ternary Complexes Containing A-A Bulge W...

New page

'''Unreleased structure'''

The entry 6d8a is ON HOLD

Authors: Liu, Y., Esyunina, D., Olovnikov, I., Teplova, M., Patel, D.J.

Description: RsAgo Ternary Complexes Containing A-A Bulge Within the Seed Segment of the Target Strand
[[Category: Unreleased Structures]]
[[Category: Esyunina, D]]
[[Category: Patel, D.J]]
[[Category: Teplova, M]]
[[Category: Olovnikov, I]]
[[Category: Liu, Y]]