6d8a

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Current revision (14:33, 13 March 2024) (edit) (undo)
 
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<StructureSection load='6d8a' size='340' side='right'caption='[[6d8a]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
<StructureSection load='6d8a' size='340' side='right'caption='[[6d8a]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6d8a]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D8A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6D8A FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6d8a]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides_ATCC_17025 Cereibacter sphaeroides ATCC 17025]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D8A FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.251&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6d8p|6d8p]], [[6d8f|6d8f]], [[6d95|6d95]], [[6d92|6d92]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d8a OCA], [http://pdbe.org/6d8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d8a RCSB], [http://www.ebi.ac.uk/pdbsum/6d8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d8a ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6d8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d8a OCA], [https://pdbe.org/6d8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d8a RCSB], [https://www.ebi.ac.uk/pdbsum/6d8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d8a ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A4WYU7_CERS5 A4WYU7_CERS5]
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Prokaryotic Argonaute (Ago) proteins were recently shown to target foreign genetic elements, thus making them a perfect model for studies of interference mechanisms. Here, we study interactions of Rhodobacter sphaeroides Ago (RsAgo) with guide RNA (gRNA) and fully complementary or imperfect target DNA (tDNA) using biochemical and structural approaches. We show that RsAgo can specifically recognize both the first nucleotide in gRNA and complementary nucleotide in tDNA, and both interactions contribute to nucleic acid binding. Non-canonical pairs and bulges on the target strand can be accommodated by RsAgo with minimal perturbation of the duplex but significantly reduce RsAgo affinity to tDNA. Surprisingly, mismatches between gRNA and tDNA induce dissociation of the guide-target duplex from RsAgo. Our results reveal plasticity in the ability of Ago proteins to accommodate helical imperfections, show how this might affect the efficiency of RNA silencing, and suggest a potential mechanism for guide release and Ago recycling.
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Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.,Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ Cell Rep. 2018 Jul 10;24(2):453-462. doi: 10.1016/j.celrep.2018.06.021. PMID:29996105<ref>PMID:29996105</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6d8a" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Cereibacter sphaeroides ATCC 17025]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Esyunina, D]]
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[[Category: Esyunina D]]
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[[Category: Liu, Y]]
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[[Category: Liu Y]]
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[[Category: Olovnikov, I]]
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[[Category: Olovnikov I]]
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[[Category: Patel, D J]]
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[[Category: Patel DJ]]
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[[Category: Teplova, M]]
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[[Category: Teplova M]]
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[[Category: Guide rna]]
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[[Category: Non-canonical base pairs and bulge]]
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[[Category: Rna binding protein]]
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[[Category: Rna-dna heteroduplex]]
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[[Category: Target dna]]
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Current revision

RsAgo Ternary Complex with guide RNA and Target DNA Containing A-A Bulge Within the Seed Segment of the Target Strand

PDB ID 6d8a

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OCA

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