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Structure of the ribosome-bound cricket paralysis virus IRES RNA

Nature Structural & Molecular Biology volume 13, pages 1092–1096 (2006)Cite this article

Abstract

Internal ribosome entry sites (IRESs) facilitate an alternative, end-independent pathway of translation initiation. A particular family of dicistroviral IRESs can assemble elongation-competent 80S ribosomal complexes in the absence of canonical initiation factors and initiator transfer RNA. We present here a cryo-EM reconstruction of a dicistroviral IRES bound to the 80S ribosome. The resolution of the cryo-EM reconstruction, in the subnanometer range, allowed the molecular structure of the complete IRES in its active, ribosome-bound state to be solved. The structure, harboring three pseudoknot-containing domains, each with a specific functional role, shows how defined elements of the IRES emerge from a compactly folded core and interact with the key ribosomal components that form the A, P and E sites, where tRNAs normally bind. Our results exemplify the molecular strategy for recruitment of an IRES and reveal the dynamic features necessary for internal initiation.

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Figure 1: Cryo-EM map of the CrPV IRES RNA in complex with the yeast 80S ribosome.
Figure 2: Structure of the CrPV IRES RNA.
Figure 3: Molecular interactions of the CRPV IRES with the 80S ribosome.
Figure 4: Comparison of the CrPV IRES with the location of the A-, P- and E-site tRNAs.

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Acknowledgements

This work was supported by a grant from the VolkswagenStiftung (to C.M.T.S.), by US National Institutes of Health grant R01 GM60635 (to P.A.P.), by the sixth EU framework program 3DEM and by the European Union and Senatsverwaltung für Wissenschaft, Forschung und Kultur Berlin (UltraStructureNetwork and Anwenderzentrum). S.R.C. was supported with a grant from the Alexander von Humboldt Stiftung.

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Authors and Affiliations

  1. Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Ziegelstrasse 5-9, Berlin, 10117, Germany

    Martin Schüler, Sean R Connell, Jan Giesebrecht, Marylena Dabrowski, Birgit Schroeer & Christian M T Spahn

  2. Architecture et Réactivité de l'ARN, Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, 15 rue R. Descartes, F-67084, Strasbourg, France

    Aurelie Lescoute & Eric Westhof

  3. UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestr. 73, Berlin, 14195, Germany

    Thorsten Mielke

  4. The University of Texas-Houston Medical School, 6431 Fannin, Houston, 77030, Texas, USA

    Pawel A Penczek

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  1. Martin Schüler
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Supplementary information

Supplementary Fig. 1

Resolution curve. (PDF 462 kb)

Supplementary Fig. 2

Comparison of the PKIII pseudoknot with the BWYV pseudoknot. (PDF 2493 kb)

Supplementary Fig. 3

Annotated secondary structure diagram. (PDF 1382 kb)

Supplementary Fig. 4

Comparison of the human telomerase pseudoknot with PKI of the CrPV IRES. (PDF 1981 kb)

Supplementary Fig. 5

Interactions of the CRPV IRES with the 80S ribosome. (PDF 2623 kb)

Supplementary Methods (PDF 41 kb)

Supplementary Notes (PDF 34 kb)

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Schüler, M., Connell, S., Lescoute, A. et al. Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat Struct Mol Biol 13, 1092–1096 (2006). https://doi.org/10.1038/nsmb1177

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