5XPA

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 9'U10' on the target strand

Summary for 5XPA

• Entry DOI: 10.2210/pdb5xpa/pdb
• Descriptor: Uncharacterized protein Ago, DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'), RNA (5'-R(P*AP*UP*AP*CP*AP*AP*CP*CP*GP*UP*UP*CP*UP*AP*CP*UP*CP*CP*G)-3'), ... (4 entities in total)
• Functional Keywords: argonaute, mirna, bulge, mismatch, dna binding protein
• Biological source: Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039); More
• Total number of polymer chains: 3
• Total formula weight: 89605.07

Authors

Sheng, G.,Gogakos, T.,Wang, J.,Zhao, H.,Serganov, A.,Juranek, S.,Tuschl, T.,Patel, J.D.,Wang, Y. (deposition date: 2017-06-01, release date: 2018-04-18, Last modification date: 2023-11-22)

Primary citation

Sheng, G.,Gogakos, T.,Wang, J.,Zhao, H.,Serganov, A.,Juranek, S.,Tuschl, T.,Patel, D.J.,Wang, Y.
Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes.
Nucleic Acids Res., 45:9149-9163, 2017

PubMed Abstract: We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bulge site, thereby having minimal impact on the cleavage site. By contrast, single-base bulges 6'U7' and 6'A7' on the target strand are looped-out of the duplex, with the resulting conformational transitions shifting the cleavable phosphate by one step. We observe a stable alignment for the looped-out 6'N7' bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson-Crick and reversed non-canonical flanking pairs. These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction.

PubMed: 28911094
DOI: 10.1093/nar/gkx547

Experimental method

X-RAY DIFFRACTION (2.9 Å)