6d8a: Difference between revisions

Revision as of 09:04, 11 November 2020

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

Structural highlights

6d8a is a 6 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ACT, MG, MPD
Related:	6d8p, 6d8f, 6d95, 6d92
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ. Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA. Cell Rep. 2018 Jul 10;24(2):453-462. doi: 10.1016/j.celrep.2018.06.021. PMID:29996105 doi:https://dx.doi.org/10.1016/j.celrep.2018.06.021

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OCA

[1] Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ. Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA. Cell Rep. 2018 Jul 10;24(2):453-462. doi: 10.1016/j.celrep.2018.06.021. PMID:29996105 doi:https://dx.doi.org/10.1016/j.celrep.2018.06.021

[1]

@@ Line 1: / Line 1: @@
 ==RsAgo Ternary Complex with guide RNA and Target DNA Containing A-A Bulge Within the Seed Segment of the Target Strand==
-<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 ==
-<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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D8A FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</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>
 <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>
-<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=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>
+<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>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 21: / Line 21: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Esyunina, D]]
 [[Category: Liu, Y]]

6d8a: Difference between revisions

Revision as of 09:04, 11 November 2020

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

Structural highlights

Publication Abstract from PubMed

References

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