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Structural basis for site-specific ribose methylation by box C/D RNA protein complexes

Abstract

Box C/D RNA protein complexes (RNPs) direct site-specific 2′-O-methylation of RNA and ribosome assembly1,2,3,4. The guide RNA in C/D RNP forms base pairs with complementary substrates and selects the modification site using a molecular ruler5,6,7. Despite many studies of C/D RNP structure8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25, the fundamental questions of how C/D RNAs assemble into RNPs and how they guide modification remain unresolved. Here we report the crystal structure of an entire catalytically active archaeal C/D RNP consisting of a bipartite C/D RNA associated with two substrates and two copies each of Nop5, L7Ae and fibrillarin at 3.15-Å resolution. The substrate pairs with the second through the eleventh nucleotide of the 12-nucleotide guide, and the resultant duplex is bracketed in a channel with flexible ends. The methyltransferase fibrillarin binds to an undistorted A-form structure of the guide–substrate duplex and specifically loads the target ribose into the active site. Because interaction with the RNA duplex alone does not determine the site specificity, fibrillarin is further positioned by non-specific and specific protein interactions. Compared with the structure of the inactive C/D RNP, extensive domain movements are induced by substrate loading. Our results reveal the organization of a monomeric C/D RNP and the mechanism underlying its site-specific methylation activity.

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Figure 1: Activity and substrate-bound structure of a C/D RNP.
Figure 2: Protein–RNA interactions in the substrate-bound C/D RNP.
Figure 3: Specific substrate recognition by fibrillarin.
Figure 4: Substrate-induced structural changes in the C/D RNP.

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Protein Data Bank

Data deposits

The atomic coordinates and structure factors are deposited in Protein Data Bank under accession number 3PLA.

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Acknowledgements

We are grateful to the staff at the Shanghai Synchrotron Radiation Facility beamline BL17U for assistance in data collection and to B. Zhu for help with the methylation assay. This research was supported by the Chinese Ministry of Science and Technology (863 grant 2008AA022310) and the Beijing Municipal Government.

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Contributions

J. Lin performed sample preparation, biochemical assays, crystallization, data collection and structure determination. S.L, R.J., A.X., L.Z and J. Lu contributed to sample preparation and crystallization at different stages of the project. J. Lin and K.Y. designed the study, analysed data and prepared the manuscript.

Corresponding author

Correspondence to Keqiong Ye.

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The authors declare no competing financial interests.

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Lin, J., Lai, S., Jia, R. et al. Structural basis for site-specific ribose methylation by box C/D RNA protein complexes. Nature 469, 559–563 (2011). https://doi.org/10.1038/nature09688

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