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Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation

Nature Structural Biology volume 9, pages 370–374 (2002)Cite this article

Abstract

The hepatitis C virus (HCV) internal ribosome entry site (IRES) RNA drives internal initiation of viral protein synthesis during host cell infection. In the tertiary structure of the IRES RNA, two helical junctions create recognition sites for direct binding of the 40S ribosomal subunit and eukaryotic initiation factor 3 (eIF3). The 2.8 Å resolution structure of the IIIabc four-way junction, which is critical for binding eIF3, reveals how junction nucleotides interact with an adjacent helix to position regions directly involved in eIF3 recognition. Two of the emergent helices stack to form a nearly continuous A-form duplex, while stacking of the other two helices is interrupted by the insertion of junction residues into the helix minor groove. This distorted stack probably serves as an important recognition surface for the translational machinery.

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Figure 1: Function of the HCV IRES and design of the crystallization construct.
Figure 2: Three-dimensional structure of the four-way RNA junction.
Figure 3: Details of the junction structure that contribute to binding site geometry.

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Acknowledgements

The authors wish to thank the NSLS X25 beamline staff and the Yale Center for Structural Biology staff for assistance in data collection and processing. We also thank L. Zhang, D.J. Battle and J.M. Murray for assistance in data collection and figure construction (DB), and A.R. Ferré-D'Amaré, R.T. Batey, R.P. Rambo and P.L. Adams for helpful discussions and advice.

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Authors and Affiliations

  1. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, 06520-8114, Connecticut, USA

    Jeffrey S. Kieft, Kaihong Zhou, Angie Grech & Jennifer A. Doudna

  2. Howard Hughes Medical Institute, Yale University, New Haven, 06520-8114, Connecticut, USA

    Jeffrey S. Kieft, Kaihong Zhou & Jennifer A. Doudna

  3. Schering-Plough Research Institute, Kenilworth, 07033-0539, New Jersey, USA

    Ronald Jubin

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  1. Jeffrey S. Kieft
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  5. Jennifer A. Doudna
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Correspondence to Jennifer A. Doudna.

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Kieft, J., Zhou, K., Grech, A. et al. Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nat Struct Mol Biol 9, 370–374 (2002). https://doi.org/10.1038/nsb781

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