5xq2: Difference between revisions
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==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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </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]] | |||
