5xq2 - Revision history

OCA at 08:09, 22 November 2023

2023-11-22T08:09:39Z

←Older revision		Revision as of 08:09, 22 November 2023
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	<StructureSection load='5xq2' size='340' side='right'caption='[[5xq2]], [[Resolution\|resolution]] 3.33Å' scene=''>		<StructureSection load='5xq2' size='340' side='right'caption='[[5xq2]], [[Resolution\|resolution]] 3.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xq2]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQ2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xq2]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] and [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XQ2 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]] 3.33Å</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=5xq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xq2 OCA], [~~http~~://pdbe.org/5xq2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xq2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xq2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xq2 ProSAT]</span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5xq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xq2 OCA], [https://pdbe.org/5xq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xq2 RCSB], [https://www.ebi.ac.uk/pdbsum/5xq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xq2 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q746M7_THET2 Q746M7_THET2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gogakos, T]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Juranek, S]]	+	[[Category: Thermus thermophilus HB27]]
-	[[Category: Patel, D]]	+	[[Category: Gogakos T]]
-	[[Category: Serganov, A]]	+	[[Category: Juranek S]]
-	[[Category: Sheng, G]]	+	[[Category: Patel D]]
-	[[Category: Tuschl, T]]	+	[[Category: Serganov A]]
-	[[Category: Wang, J]]	+	[[Category: Sheng G]]
-	[[Category: Wang, Y]]	+	[[Category: Tuschl T]]
-	[[Category: Zhao, H]]	+	[[Category: Wang J]]
-	~~[[Category: Argonaute]]~~	+	[[Category: Wang Y]]
-	~~[[Category: Bulge]]~~	+	[[Category: Zhao H]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Mirna]]~~	+
-	~~[[Category: Mismatch~~]]	+

OCA at 06:56, 14 October 2020

2020-10-14T06:56:47Z

←Older revision		Revision as of 06:56, 14 October 2020
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	==Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 on the guide strand==		==Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 on the guide strand==
-	<StructureSection load='5xq2' size='340' side='right' caption='[[5xq2]], [[Resolution\|resolution]] 3.33Å' scene=''>	+	<StructureSection load='5xq2' size='340' side='right'caption='[[5xq2]], [[Resolution\|resolution]] 3.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xq2]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xq2]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XQ2 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='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=5xq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xq2 OCA], [http://pdbe.org/5xq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xq2 RCSB], [http://www.ebi.ac.uk/pdbsum/5xq2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xq2 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=5xq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xq2 OCA], [http://pdbe.org/5xq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xq2 RCSB], [http://www.ebi.ac.uk/pdbsum/5xq2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xq2 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: Gogakos, T]]		[[Category: Gogakos, T]]
	[[Category: Juranek, S]]		[[Category: Juranek, S]]

OCA at 09:31, 4 October 2017

2017-10-04T09:31:23Z

←Older revision		Revision as of 09:31, 4 October 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5xq2 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 on the guide strand==
		+	<StructureSection load='5xq2' size='340' side='right' caption='[[5xq2]], [[Resolution\|resolution]] 3.33Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xq2]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XQ2 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>
		+	<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=5xq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xq2 OCA], [http://pdbe.org/5xq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xq2 RCSB], [http://www.ebi.ac.uk/pdbsum/5xq2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xq2 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bulge site, thereby having minimal impact on the cleavage site. By contrast, single-base bulges 6'U7' and 6'A7' on the target strand are looped-out of the duplex, with the resulting conformational transitions shifting the cleavable phosphate by one step. We observe a stable alignment for the looped-out 6'N7' bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson-Crick and reversed non-canonical flanking pairs. These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction.

-	~~Authors~~:	+	Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes.,Sheng G, Gogakos T, Wang J, Zhao H, Serganov A, Juranek S, Tuschl T, Patel DJ, Wang Y Nucleic Acids Res. 2017 Sep 6;45(15):9149-9163. doi: 10.1093/nar/gkx547. PMID:28911094<ref>PMID:28911094</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xq2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gogakos, T]]
		+	[[Category: Juranek, S]]
		+	[[Category: Patel, D]]
		+	[[Category: Serganov, A]]
		+	[[Category: Sheng, G]]
		+	[[Category: Tuschl, T]]
		+	[[Category: Wang, J]]
		+	[[Category: Wang, Y]]
		+	[[Category: Zhao, H]]
		+	[[Category: Argonaute]]
		+	[[Category: Bulge]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Mirna]]
		+	[[Category: Mismatch]]

OCA: Protected "5xq2" [edit=sysop:move=sysop]

2017-09-27T15:40:09Z

Protected "5xq2" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:40, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xq2 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2017-09-27T15:40:08Z

New page: '''Unreleased structure''' The entry 5xq2 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xq2 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]