Structure of the ribosome-bound cricket paralysis virus IRES RNA (original) (raw)

• Sonenberg, N. & Dever, T.E. Eukaryotic translation initiation factors and regulators. Curr. Opin. Struct. Biol. 13, 56–63 (2003).
  Article CAS Google Scholar
• Dever, T.E. Gene-specific regulation by general translation factors. Cell 108, 545–556 (2002).
  Article CAS Google Scholar
• Hellen, C.U. & Sarnow, P. Internal ribosome entry sites in eukaryotic mRNA molecules. Genes Dev. 15, 1593–1612 (2001).
  Article CAS Google Scholar
• Vagner, S., Galy, B. & Pyronnet, S. Irresistible IRES: attracting the translation machinery to internal ribosome entry sites. EMBO Rep. 2, 893–898 (2001).
  Article CAS Google Scholar
• Stoneley, M. & Willis, A.E. Cellular internal ribosome entry segments: structures, trans-acting factors and regulation of gene expression. Oncogene 23, 3200–3207 (2004).
  Article CAS Google Scholar
• Jackson, R.J. Alternative mechanisms of initiating translation of mammalian mRNAs. Biochem. Soc. Trans. 33, 1231–1241 (2005).
  Article CAS Google Scholar
• Sasaki, J. & Nakashima, N. Methionine-independent initiation of translation in the capsid protein of an insect RNA virus. Proc. Natl. Acad. Sci. USA 97, 1512–1515 (2000).
  Article CAS Google Scholar
• Pestova, T.V. & Hellen, C.U. Translation elongation after assembly of ribosomes on the Cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA. Genes Dev. 17, 181–186 (2003).
  Article CAS Google Scholar
• Wilson, J.E., Pestova, T.V., Hellen, C.U. & Sarnow, P. Initiation of protein synthesis from the A site of the ribosome. Cell 102, 511–520 (2000).
  Article CAS Google Scholar
• Jan, E., Goss Kinzy, T. & Sarnow, P. Divergent tRNA-like element supports initiation, elongation and termination of protein biosynthesis. Proc. Natl. Acad. Sci. USA 100, 15410–15415 (2003).
  Article CAS Google Scholar
• Spahn, C.M.T. et al. Hepatitis C virus IRES RNA-induced changes in the conformation of the 40S ribosomal subunit. Science 291, 1962 (2001).
  Article Google Scholar
• Spahn, C.M. et al. Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor. Cell 118, 465–475 (2004).
  Article CAS Google Scholar
• Thompson, S.R., Gulyas, K.D. & Sarnow, P. Internal initiation in Saccharomyces cerevisiae mediated by an initiator tRNA/eIF2-independent internal ribosome entry site element. Proc. Natl. Acad. Sci. USA 98, 12972–12977 (2001).
  Article CAS Google Scholar
• Halic, M., Becker, T., Frank, J., Spahn, C.M. & Beckmann, R. Localization and dynamic behavior of ribosomal protein L30e. Nat. Struct. Mol. Biol. 12, 467–468 (2005).
  Article CAS Google Scholar
• Spahn, C.M. et al. Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J. 23, 1008–1019 (2004).
  Article CAS Google Scholar
• Jan, E. & Sarnow, P. Factorless ribosome assembly on the internal ribosome entry site of cricket paralysis virus. J. Mol. Biol. 324, 889–902 (2002).
  Article CAS Google Scholar
• Nishiyama, T. et al. Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes. Nucleic Acids Res. 31, 2434–2442 (2003).
  Article CAS Google Scholar
• Kanamori, Y. & Nakashima, N. A tertiary structure model of the internal ribosome entry site (IRES) for methionine-independent initiation of translation. RNA 7, 266–274 (2001).
  Article CAS Google Scholar
• Pestova, T.V., Lomakin, I.B. & Hellen, C.U. Position of the CrPV IRES on the 40S subunit and factor dependence of IRES/80S ribosome assembly. EMBO Rep. 5, 906–913 (2004).
  Article CAS Google Scholar
• Hilbers, C.W., Michiels, P.J. & Heus, H.A. New developments in structure determination of pseudoknots. Biopolymers 48, 137–153 (1998).
  Article CAS Google Scholar
• Su, L., Chen, L., Egli, M., Berger, J.M. & Rich, A. Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nat. Struct. Biol. 6, 285–292 (1999).
  Article CAS Google Scholar
• Battle, D.J. & Doudna, J.A. Specificity of RNA-RNA helix recognition. Proc. Natl. Acad. Sci. USA 99, 11676–11681 (2002).
  Article CAS Google Scholar
• Nissen, P., Ippolito, J.A., Ban, N., Moore, P.B. & Steitz, T.A. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl. Acad. Sci. USA 98, 4899–4903 (2001).
  Article CAS Google Scholar
• Costantino, D. & Kieft, J.S. A preformed compact ribosome-binding domain in the cricket paralysis-like virus IRES RNAs. RNA 11, 332–343 (2005).
  Article CAS Google Scholar
• Theimer, C.A., Blois, C.A. & Feigon, J. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol. Cell 17, 671–682 (2005).
  Article CAS Google Scholar
• Yusupov, M.M. et al. Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883–896 (2001).
  Article CAS Google Scholar
• Spahn, C.M.T. et al. Structure of the 80S ribosome from _Saccharomyces cerevisiae_—tRNA-ribosome and subunit-subunit interactions. Cell 107, 373–386 (2001).
  Article CAS Google Scholar
• Harms, J. et al. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107, 679–688 (2001).
  Article CAS Google Scholar
• Valle, M. et al. Locking and unlocking of ribosomal motions. Cell 114, 123–134 (2003).
  Article CAS Google Scholar
• Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905–920 (2000).
  Article CAS Google Scholar
• Bottcher, B., Wynne, S.A. & Crowther, R.A. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature 386, 88–91 (1997).
  Article CAS Google Scholar
• Chiu, W., Baker, M.L., Jiang, W., Dougherty, M. & Schmid, M.F. Electron cryomicroscopy of biological machines at subnanometer resolution. Structure 13, 363–372 (2005).
  Article CAS Google Scholar
• Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 (1996).
  Article CAS Google Scholar
• Massire, C. & Westhof, E. MANIP: an interactive tool for modelling RNA. J. Mol. Graph. Model. 16, 197–205 255–7 (1998).
  Article CAS Google Scholar
• Jones, T.A. & Kjeldgaard, M. Electron density map interpretation. Methods Enzymol. 277B, 173–207 (1997).
  Article Google Scholar