6u8d | pdb_00006u8d

Crystal structure of hepatitis C virus IRES junction IIIabc in complex with Fab HCV2

spinqualitylabelsall models 6u8d, resolution 1.81Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6u8d is a 3 chain structure with sequence from Hepacivirus C and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.807Å Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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-A and 2.75-A 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. Synthetic antibody binding to a pre-organized IRES RNA domain of hepatitis C virus inhibits translation.,Koirala D, Lewicka A, Koldobskaya Y, Huang H, Piccirilli JA ACS Chem Biol. 2019 Nov 25. doi: 10.1021/acschembio.9b00785. PMID:31765566 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Antibody 3D structures

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