4ncb: Difference between revisions
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== | ==Structure of Thermus thermophilus Argonaute bound to guide DNA and 19-mer target DNA with Mg2+== | ||
[[4ncb]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCB OCA]. | <StructureSection load='4ncb' size='340' side='right' caption='[[4ncb]], [[Resolution|resolution]] 2.19Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4ncb]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NCB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NCB 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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4n41|4n41]], [[4n47|4n47]], [[4n76|4n76]], [[4nca|4nca]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Argonaute, TT_P0026 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=4ncb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ncb OCA], [http://pdbe.org/4ncb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ncb RCSB], [http://www.ebi.ac.uk/pdbsum/4ncb PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We report on crystal structures of ternary Thermus thermophilus Argonaute (TtAgo) complexes with 5'-phosphorylated guide DNA and a series of DNA targets. These ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 A have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of Mg2+ cations, and the putative water nucleophile positioned for in-line attack on the cleavable phosphate for TtAgo-mediated target cleavage by a RNase H-type mechanism. In addition, these ternary complex structures have provided insights into protein and DNA conformational changes that facilitate transition between cleavage-incompatible and cleavage-compatible states, including the role of a Glu finger in generating a cleavage-competent catalytic Asp-Glu-Asp-Asp tetrad. Following cleavage, the seed segment forms a stable duplex with the complementary segment of the target strand. | |||
Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.,Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y Proc Natl Acad Sci U S A. 2013 Dec 27. PMID:24374628<ref>PMID:24374628</ref> | |||
<ref | |||
[[Category: Rao, Y | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
[[Category: Sheng, G | </div> | ||
[[Category: Wang, J | <div class="pdbe-citations 4ncb" style="background-color:#fffaf0;"></div> | ||
[[Category: Wang, Y | |||
[[Category: Zhao, H | ==See Also== | ||
*[[Argonaute|Argonaute]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Flavobacterium thermophilum yoshida and oshima 1971]] | |||
[[Category: Rao, Y]] | |||
[[Category: Sheng, G]] | |||
[[Category: Wang, J]] | |||
[[Category: Wang, Y]] | |||
[[Category: Zhao, H]] | |||
[[Category: Argonaute]] | [[Category: Argonaute]] | ||
[[Category: Dna interference]] | [[Category: Dna interference]] | ||