Extended Data Figure 7: Molecular interactions of the CSFV ΔII-IRES with the 40S subunit and interactions of eIF3 with the HCV and CSFV IRESs.
From: Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit

a, Secondary structure diagram of the CSFV ΔII-IRES, with nucleotides shown in different degrees of bold to show qualitatively their flexibility in the cryo-electron microscopy map (the more flexible, the bolder). Circled nucleotides interact with the indicated components of the 40S subunit. Ribosomal protein names and residue numbers are indicated according to the Tetrahymena thermophila 40S subunit42. b–d, Secondary structure diagram of the apical region of domain III of the CSFV IRES (b, c) and the HCV IRES (d). b, Contacts of eIF3 with the IRES in the cryoEM map of the 40S–ΔII-IRES–eIF3 complex. c, d, Sites of strong protection of CSFV and HCV IRESs by native eIF3 from enzymatic cleavage and chemical modification, of protection of the HCV IRES by a 10-subunit form of eIF3 from 1M7 modification, or of interference with binding of eIF3 to the IRES by modification, as indicated in the keys5,9,11. Abbreviations: dimethyl sulphate (DMS), 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluene sulphonate (CMCT), diethylpyrocarbonate (DEPC), 1-methyl-7-nitroisatoic anhydride (1M7). The inset panels show CSFV(c) and HCV IRESs (d), with helix III4 and subdomains IIIa, IIIb and IIIc in bold.