We have determined the solution structure of the complex between an arginine-glycine-rich RGG peptide from the human fragile X mental retardation protein (FMRP) and an in vitro–selected guanine-rich (G-rich) sc1 RNA. The bound RNA forms a newly discovered G-quadruplex separated from the flanking duplex stem by a mixed junctional tetrad. The RGG peptide is positioned along the major groove of the RNA duplex, with the G-quadruplex forcing a sharp turn of R10GGGGR15 at the duplex-quadruplex junction. Arg10 and Arg15 form cross-strand specificity–determining intermolecular hydrogen bonds with the major-groove edges of guanines of adjacent Watson-Crick G•C pairs. Filter-binding assays on RNA and peptide mutations identify and validate contributions of peptide-RNA intermolecular contacts and shape complementarity to molecular recognition. These findings on FMRP RGG domain recognition by a combination of G-quadruplex and surrounding RNA sequences have implications for the recognition of other genomic G-rich RNAs.
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We thank Y. Gosser and S. Pitt (Memorial Sloan-Kettering Cancer Center) for their participation at the early stage of the project, O. Mostovetsky, E.F. Stone and K.Y.S. Hung (Rockefeller University) for technical assistance, and A. Lash (Memorial Sloan-Kettering Cancer Center) for bioinformatics of the RG4R motif in the human genome. This research was supported by US National Institutes of Health grants CA049982 (to D.J.P.) and R01 HD040647 (to J.C.D.) and Singapore Biomedical Research Council grant 07/1/22/19/542 to A.T.P. D.J.P. is a member of the New York Structural Biology Center, supported by US National Institutes of Health grant GM66354.
The authors declare no competing financial interests.
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Phan, A., Kuryavyi, V., Darnell, J. et al. Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction. Nat Struct Mol Biol 18, 796–804 (2011). https://doi.org/10.1038/nsmb.2064
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