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Structural basis for exon recognition by a group II intron

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Abstract

Free group II introns are infectious retroelements that can bind and insert themselves into RNA and DNA molecules via reverse splicing. Here we report the 3.4-Å crystal structure of a complex between an oligonucleotide target substrate and a group IIC intron, as well as the refined free intron structure. The structure of the complex reveals the conformation of motifs involved in exon recognition by group II introns.

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Figure 1: The refined structure of the group II intron cocrystallized with exon substrate reveals additional structural features such as the coordination loop, additional regions of stems Id1 and Id2, κ−κ′ (all highlighted by background space-filling models; see also Supplementary Fig. 1) and the cocrystallized exon junction target (pink ribbon).
Figure 2: Exon recognition and metal-ion coordination within the intron core.

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Acknowledgements

We thank the staff of the NE-CAT beamline 24-ID-C at the Advanced Photon Source of Argonne National Laboratory. We also thank O. Fedorova for advice and support. This work was supported by the Howard Hughes Medical Institute (HHMI) and US National Institutes of Health grant GM50313 (A.M.P.). N.T. and A.M.P. are funded by the HHMI.

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Authors and Affiliations

  1. Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut, 06520, USA

    Navtej Toor & Anna Marie Pyle

  2. Howard Hughes Medical Institute, Yale University, 266 Whitney Avenue, New Haven, Connecticut, 06520, USA

    Navtej Toor & Anna Marie Pyle

  3. The Northeastern Collaborative Access Team (NE-CAT) at the Advanced Photon Source at Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois, 60439, USA

    Kanagalaghatta Rajashankar

  4. Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Avenue, New Haven, Connecticut, 06511, USA

    Kevin S Keating

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  1. Navtej Toor
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  2. Kanagalaghatta Rajashankar
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  3. Kevin S Keating
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  4. Anna Marie Pyle
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Corresponding authors

Correspondence to Kanagalaghatta Rajashankar or Anna Marie Pyle.

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Supplementary Figures 1 and 2, Supplementary Table 1 and Supplementary Methods (PDF 1705 kb)

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Toor, N., Rajashankar, K., Keating, K. et al. Structural basis for exon recognition by a group II intron. Nat Struct Mol Biol 15, 1221–1222 (2008). https://doi.org/10.1038/nsmb.1509

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