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Nucleic Acids Research Advance Access originally published online on January 7, 2009
Nucleic Acids Research 2009 37(4):1141-1151; doi:10.1093/nar/gkn1026
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Nucleic Acids Research, 2009, Vol. 37, No. 4 1141-1151
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Positioning of subdomain IIId and apical loop of domain II of the hepatitis C IRES on the human 40S ribosome

Elena Babaylova1, Dmitri Graifer1, Alexey Malygin1, Joachim Stahl2, Ivan Shatsky3 and Galina Karpova1,*

1Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia, 2Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin-Buch, 13092 Berlin, Germany and 3Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119899, Russia

*To whom correspondence should be addressed. Tel: +7 383 335 62 29; Fax: +7 383 333 36 77; Email: karpova{at}niboch.nsc.ru

Received September 11, 2008. Revised November 19, 2008. Accepted December 9, 2008.

The 5'-untranslated region of the hepatitis C virus (HCV) RNA contains a highly structured motif called IRES (Internal Ribosome Entry Site) responsible for the cap-independent initiation of the viral RNA translation. At first, the IRES binds to the 40S subunit without any initiation factors so that the initiation AUG codon falls into the P site. Here using an original site-directed cross-linking strategy, we identified 40S subunit components neighboring subdomain IIId, which is critical for HCV IRES binding to the subunit, and apical loop of domain II, which was suggested to contact the 40S subunit from data on cryo-electron microscopy of ribosomal complexes containing the HCV IRES. HCV IRES derivatives that bear a photoactivatable group at nucleotide A275 or at G263 in subdomain IIId cross-link to ribosomal proteins S3a, S14 and S16, and HCV IRES derivatized at the C83 in the apex of domain II cross-link to proteins S14 and S16.


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