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5xpg
From Proteopedia
(Difference between revisions)
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==Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 6'U7' on the target strand== | ==Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 6'U7' on the target strand== | ||
| - | <StructureSection load='5xpg' size='340' side='right' caption='[[5xpg]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='5xpg' size='340' side='right'caption='[[5xpg]], [[Resolution|resolution]] 2.80Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5xpg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XPG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XPG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5xpg]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XPG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XPG 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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dlb|3dlb]], [[3dlh|3dlh]], [[3f73|3f73]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dlb|3dlb]], [[3dlh|3dlh]], [[3f73|3f73]]</td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TT_P0026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</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=5xpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xpg OCA], [http://pdbe.org/5xpg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xpg RCSB], [http://www.ebi.ac.uk/pdbsum/5xpg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xpg ProSAT]</span></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=5xpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xpg OCA], [http://pdbe.org/5xpg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xpg RCSB], [http://www.ebi.ac.uk/pdbsum/5xpg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xpg ProSAT]</span></td></tr> | ||
</table> | </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> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5xpg" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Thet2]] | ||
[[Category: Gogakos, T]] | [[Category: Gogakos, T]] | ||
[[Category: Juranek, S]] | [[Category: Juranek, S]] | ||
Revision as of 09:02, 1 May 2019
Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 6'U7' on the target strand
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Categories: Large Structures | Thet2 | Gogakos, T | Juranek, S | Patel, J D | Serganov, A | Sheng, G | Tuschl, T | Wang, J | Wang, Y | Zhao, H | Argonaute | Bulge | Dna binding protein | Mirna | Mismatch
