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Nat Chem Biol. 2015 Dec;11(12):967-72. doi: 10.1038/nchembio.1949. Epub 2015 Oct 26.

Crystal structure of group II intron domain 1 reveals a template for RNA assembly.

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Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
Northeastern Collaborative Access Team (NE-CAT), Argonne National Laboratory, Argonne, Illinois, USA.
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA.
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.
Department of Chemistry, Yale University, New Haven, Connecticut, USA.
Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.


Although the importance of large noncoding RNAs is increasingly appreciated, our understanding of their structures and architectural dynamics remains limited. In particular, we know little about RNA folding intermediates and how they facilitate the productive assembly of RNA tertiary structures. Here, we report the crystal structure of an obligate intermediate that is required during the earliest stages of group II intron folding. Composed of domain 1 from the Oceanobacillus iheyensis group II intron (266 nucleotides), this intermediate retains native-like features but adopts a compact conformation in which the active site cleft is closed. Transition between this closed and the open (native) conformation is achieved through discrete rotations of hinge motifs in two regions of the molecule. The open state is then stabilized by sequential docking of downstream intron domains, suggesting a 'first come, first folded' strategy that may represent a generalizable pathway for assembly of large RNA and ribonucleoprotein structures.

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