6D9K

Ternary RsAgo Complex with Guide RNA and Target DNA Containing A-G Non-canonical Pair

Summary for 6D9K

• Entry DOI: 10.2210/pdb6d9k/pdb
• Related: 6D8A 6D8F 6D8P 6D92 6D95
• Descriptor: Uncharacterized protein, RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3'), DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*GP*GP*CP*AP*GP*TP*AP*AP*C)-3'), ... (7 entities in total)
• Functional Keywords: guide rna, target dna, rna-dna heteroduplex, non-canonical base pairs and bulges, rna binding protein, rna binding protein-rna-dna complex, rna binding protein/rna/dna
• Biological source: Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3); More
• Total number of polymer chains: 6
• Total formula weight: 204807.30

Authors

Liu, Y.,Esyunina, D.,Olovnikov, I.,Teplova, M.,Patel, D.J. (deposition date: 2018-04-30, release date: 2018-07-25, Last modification date: 2024-03-13)

Primary citation

Liu, Y.,Esyunina, D.,Olovnikov, I.,Teplova, M.,Kulbachinskiy, A.,Aravin, A.A.,Patel, D.J.
Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.
Cell Rep, 24:453-462, 2018

PubMed Abstract: 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.

PubMed: 29996105
DOI: 10.1016/j.celrep.2018.06.021

Experimental method

X-RAY DIFFRACTION (2 Å)