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Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot

Nature Structural Biology volume 6, pages 285–292 (1999)Cite this article

Abstract

Many viruses regulate translation of polycistronic mRNA using a -1 ribosomal frameshift induced by an RNA pseudoknot. A pseudoknot has two stems that form a quasi-continuous helix and two connecting loops. A 1.6 Å crystal structure of the beet western yellow virus (BWYV) pseudoknot reveals rotation and a bend at the junction of the two stems. A loop base is inserted in the major groove of one stem with quadruple-base interactions. The second loop forms a new minor-groove triplex motif with the other stem, involving 2'-OH and triple-base interactions, as well as sodium ion coordination. Overall, the number of hydrogen bonds stabilizing the tertiary interactions exceeds the number involved in Watson–Crick base pairs. This structure will aid mechanistic analyses of ribosomal frameshifting.

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Figure 1: Beet western yellow virus (BWYV) pseudoknot electron density maps at 1.9 Å resolution contoured at 1.0σ above the mean.
Figure 2: The beet western yellow virus (BWYV) pseudoknot crystal structure and secondary sequence.
Figure 3: RNA triplex interactions of loop 2 in the minor groove of stem 1.
Figure 5: Stereo view of stabilizing interactions at sharp turns, ions and water molecules.
Figure 4: Quadruple-base interactions of loop 1.

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Acknowledgements

We thank E. de La Fortelle for extensive help on the program SHARP; G. Minasov and I. Berger for help in data processing and refinement, Y.-G. Kim for frameshifting discussions; C. Ogata (X4A-NSLS), M. Soltis (SSRL) and the staff at CHESS F2 for synchrotron assistance. We acknowledge help from T. Schwartz, D. Chan, M. Schade and K.-J. Wu on data collection; V. Tereshko, A. and H. Szoke for technical assistance; J. Cate, D. Bartel, M. Rould, U. RajBhandary, A. Herbert and B. Brown for helpful discussions. We are indebted to H. Taube and S. Holbrook for providing us with the osmium hexammine triflate compound; J. McCloskey and P. Crain for bromine mass spectroscopy analysis. We also thank L. Gerhke, K. Lowenhaupt and F. Houser-Scott for assistance in the T7 transcription system; D. Lauffenburger and S. Zhang at the MIT Center of Biomedical Engineering for providing the computer facility. This research was supported by grants from the National Science Foundation, the National Institutes of Health, the National Foundation for Cancer Research and the National Aeronautics and Space Administration.

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  1. Liqing Chen

    Present address: Laboratory for Structural Biology, Department of Chemistry and Materials Science, University of Alabama, Huntsville, Alabama, 35899 , USA

  2. James M. Berger

    Present address: Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720, USA

Authors and Affiliations

  1. Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Li Su, Liqing Chen & Alexander Rich

  2. Department of Molecular Pharmacology & Biological Chemistry and the Drug Discovery Program, Northwestern University Medical School, Chicago, 60611, Illinois, USA

    Martin Egli

  3. Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    James M. Berger

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Su, L., Chen, L., Egli, M. et al. Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nat Struct Mol Biol 6, 285–292 (1999). https://doi.org/10.1038/6722

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