Viral RNA-peptide structures

We are interested in investigating the high resolution three dimensional structure of RNA-protein complexes from AMV and ilarviruses. Previously we identified a high affinity 39 nucleotide binding site at the extreme 3' end of the AMV 3' UTR as well as a conserved PTxRSxxY RNA binding domain within the N-terminus of the viral coat protein. We recently solved the structure of this RNA-protein complex by xray crystallographic methods, in collaboration with Jim Hogle's laboratory.

The structure shows that the AMV 3’ terminal RNA (39nt) forms two hairpins. Additionally, each of the two RNA duplexes is extended by base pairing interactions involving the AUGC sequences previously believed to be single stranded regions separating the hairpins. In each case, the extended stack is capped by a conserved aromatic side-chain from the peptide, and stabilized by contacts with a conserved arginine. This unusual RNA folding motif introduces a kink into the RNA, placing the hairpins at nearly right angles. Mutation of the base identity or arrangement of the AUGC sequences eliminates peptide binding to the RNA when examined by electrophoretic mobility gel shift assays. The 3’ UTR of AMV contains a number of AUGC sequences separating putative hairpins. It is possible that the unique RNA fold identified in this structure serves as a module for folding the entire 3’ UTR into a compact form required for replicase recognition.

The HCV RNA 3' UTR-RIGI complex is being evaluated for potential co-crystal structure analysis.