title: Proteins surrounding hairpin IIIe of the hepatitis C virus internal ribosome entry site on the human 40S ribosomal subunit.
abstract: Binding of the internal ribosome entry site (IRES) of the hepatitis C virus (HCV) RNA to the eIF-free 40S ribosomal subunit is the first step of initiation of translation of the viral RNA. Hairpins IIId and IIIe comprising 253-302 nt of the IRES are known to be essential for binding to the 40S subunit. Here we have examined the molecular environment of the HCV IRES in its binary complex with the human 40S ribosomal subunit. For this purpose, two RNA derivatives were used that bore a photoactivatable perfluorophenyl azide cross-linker. In one derivative the cross-linker was at the nucleotide A296 in hairpin IIIe, and in the other at G87 in domain II. Site-specific introduction of the cross-linker was performed using alkylating derivatives of oligodeoxyribonucleotides complementary to the target RNA sequences. No cross-links with the rRNA were detected with either RNA derivative. The RNA with the photoactivatable group at A296 cross-linked to proteins identified as S5 and S16 (major) and p40 and S3a (minor), while no cross-links with proteins were detected with RNA modified at G87. The results obtained indicate that hairpin IIIe is located on the solvent side of the 40S subunit head on a site opposite the beak.
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
authors.forename: Elena
authors.initials: E
authors.lastname: Laletina
authors.forename: Dmitri
authors.initials: D
authors.lastname: Graifer
authors.forename: Alexey
authors.initials: A
authors.lastname: Malygin
authors.forename: Anton
authors.initials: A
authors.lastname: Ivanov
authors.forename: Ivan
authors.initials: I
authors.lastname: Shatsky
authors.forename: Galina
authors.initials: G
authors.lastname: Karpova
mesh_terms: D020121:5' Untranslated Regions / Q000737:chemistry*; D001483:Base Sequence; D003432:Cross-Linking Reagents; D016174:Hepacivirus / Q000235:genetics*; D006801:Humans; D008027:Light; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010442:Peptide Chain Initiation, Translational; D012367:RNA, Viral / Q000737:chemistry*; D012269:Ribosomal Proteins / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry
chemical_list: D020121:5' Untranslated Regions; D003432:Cross-Linking Reagents; D012367:RNA, Viral; D012269:Ribosomal Proteins