8ffi: Difference between revisions

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-'''Unreleased structure'''
-The entry 8ffi is ON HOLD  until Paper Publication
+==Structure of tetramerized MapSPARTA upon guide RNA-mediated target DNA binding==
+<StructureSection load='8ffi' size='340' side='right'caption='[[8ffi]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8ffi]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Maribacter_polysiphoniae Maribacter polysiphoniae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8FFI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8FFI FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.7&#8491;</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=8ffi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ffi OCA], [https://pdbe.org/8ffi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ffi RCSB], [https://www.ebi.ac.uk/pdbsum/8ffi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ffi ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A316E683_9FLAO A0A316E683_9FLAO]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+While eukaryotic Argonautes and long prokaryotic Argonautes (pAgos) cleave nucleic acids, some short pAgos lack nuclease activity and hydrolyze NAD(P)(+) to induce bacterial cell death(1). We present a hierarchical activation pathway for SPARTA, a short pAgo consisting of an Ago protein and an associated protein TIR-APAZ(2). SPARTA progresses through distinct oligomeric forms, including a monomeric apo state, a monomeric RNA/DNA-bound state, two dimeric RNA/DNA-bound states, and a tetrameric RNA/DNA-bound active state. These snapshots together identify oligomerization as a mechanistic principle of SPARTA activation. Apo SPARTA is inactive, its RNA/DNA-binding channel occupied an auto-inhibitory motif in TIR-APAZ. Upon RNA/DNA binding, SPARTA transitions from a monomer to a symmetric and then an asymmetric dimer, in which two TIR domains interact via charge and shape complementarity. Next, two dimers assemble into a tetramer with a central TIR cluster responsible for hydrolyzing NAD(P)(+). Additionally, we observed unique features of SPARTA-RNA/DNA interactions, including competition between the DNA 3' end and the auto-inhibitory motif, interactions between the RNA G2 nucleotide and Ago, and splaying of the RNA-DNA duplex by two loops exclusive to short pAgos. Together, our findings contribute a mechanistic basis for the activation of short pAgos, a large section of the Ago superfamily.
-Authors:
+Oligomerization-mediated activation of a short prokaryotic Argonaute.,Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM Nature. 2023 Jul 26. doi: 10.1038/s41586-023-06456-z. PMID:37494956<ref>PMID:37494956</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8ffi" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Maribacter polysiphoniae]]
+[[Category: Synthetic construct]]
+[[Category: Fu TM]]
+[[Category: Shen ZF]]
+[[Category: Yang XY]]