SNAP output for PDB entry 6u8k [SNAP web server]

PDB-id

6u8k; SNAP-derived features in text and JSON formats; DNAproDB

Class

RNA-immune system

Method

X-ray (2.75 Å)

Summary

Crystal structure of hepatitis c virus ires junction iiiabc in complex with fab hcv3

Reference

Koirala D, Lewicka A, Koldobskaya Y, Huang H, Piccirilli JA (2020): "Synthetic Antibody Binding to a Preorganized RNA Domain of Hepatitis C Virus Internal Ribosome Entry Site Inhibits Translation." Acs Chem.Biol., 15, 205-216. doi: 10.1021/acschembio.9b00785.

Abstract

Structured RNA elements within the internal ribosome entry site (IRES) of hepatitis C virus (HCV) genome hijack host cell machinery for translation initiation through a cap-independent mechanism. Here, using a phage display selection, we obtained two antibody fragments (Fabs), HCV2 and HCV3, against HCV IRES that bind the RNA with dissociation constants of 32 ± 7 nM and 37 ± 8 nM respectively, specifically recognizing the so-called junction IIIabc (JIIIabc). We used these Fabs as crystallization chaperones and determined the high-resolution crystal structures of JIIIabc - HCV2 and - HCV3 complexes at 1.81-Å and 2.75-Å resolution respectively, revealing an anti-parallel four-way junction with the so-called IIIa and IIIc sub-domains brought together through tertiary interactions. The RNA conformation observed in the structures supports the structural model for this region derived from cryo-EM data for the HCV IRES - 40S ribosome complex, suggesting that the tertiary fold of the RNA pre-organizes the domain for interactions with the 40S ribosome. Strikingly, both Fabs and the ribosomal protein eS27 not only interact with a common subset of nucleotides within the JIIIabc but also use physio-chemically similar sets of protein residues to do so, suggesting that the RNA surface is well-suited for interactions with proteins, perhaps analogous to the 'hot spot' concept elaborated for protein-protein interactions. Using a rabbit reticulocyte lysate-based translation assay with a bicistronic reporter construct, we further demonstrated that Fabs HCV2 and HCV3 specifically inhibit the HCV IRES-directed translation, implicating disruption of the JIIIabc - ribosome interaction as a potential therapeutic strategy against HCV.