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


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.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

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


  1. Venema, J. & Tollervey, D. Ribosome synthesis in Saccharomyces cerevisiae . Annu. Rev. Genet. 33, 261–311 (1999)

    CAS  Article  Google Scholar 

  2. Kiss, T. Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J. 20, 3617–3622 (2001)

    CAS  Article  Google Scholar 

  3. Reichow, S. L., Hamma, T., Ferre-D’Amare, A. R. & Varani, G. The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res. 35, 1452–1464 (2007)

    CAS  Article  Google Scholar 

  4. Henras, A. K. et al. The post-transcriptional steps of eukaryotic ribosome biogenesis. Cell. Mol. Life Sci. 65, 2334–2359 (2008)

    CAS  Article  Google Scholar 

  5. Cavaille, J., Nicoloso, M. & Bachellerie, J. P. Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 383, 732–735 (1996)

    ADS  CAS  Article  Google Scholar 

  6. Kiss-Laszlo, Z., Henry, Y., Bachellerie, J. P., Caizergues-Ferrer, M. & Kiss, T. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85, 1077–1088 (1996)

    CAS  Article  Google Scholar 

  7. Tycowski, K. T., Smith, C. M., Shu, M. D. & Steitz, J. A. A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus . Proc. Natl Acad. Sci. USA 93, 14480–14485 (1996)

    ADS  CAS  Article  Google Scholar 

  8. Omer, A. D. et al. Homologs of small nucleolar RNAs in Archaea. Science 288, 517–522 (2000)

    ADS  CAS  Article  Google Scholar 

  9. Wang, H., Boisvert, D., Kim, K. K., Kim, R. & Kim, S. H. Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution. EMBO J. 19, 317–323 (2000)

    CAS  Article  Google Scholar 

  10. Vidovic, I., Nottrott, S., Hartmuth, K., Luhrmann, R. & Ficner, R. Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. Mol. Cell 6, 1331–1342 (2000)

    CAS  Article  Google Scholar 

  11. Watkins, N. J. et al. A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP. Cell 103, 457–466 (2000)

    CAS  Article  Google Scholar 

  12. Cahill, N. M. et al. Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP. EMBO J. 21, 3816–3828 (2002)

    CAS  Article  Google Scholar 

  13. Omer, A. D., Ziesche, S., Ebhardt, H. & Dennis, P. P. In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex. Proc. Natl Acad. Sci. USA 99, 5289–5294 (2002)

    ADS  CAS  Article  Google Scholar 

  14. Aittaleb, M. et al. Structure and function of archaeal box C/D sRNP core proteins. Nature Struct. Biol. 10, 256–263 (2003)

    CAS  Article  Google Scholar 

  15. Rashid, R. et al. Functional requirement for symmetric assembly of archaeal box C/D small ribonucleoprotein particles. J. Mol. Biol. 333, 295–306 (2003)

    CAS  Article  Google Scholar 

  16. Tran, E. J., Zhang, X. & Maxwell, E. S. Efficient RNA 2′-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C′/D′ RNPs. EMBO J. 22, 3930–3940 (2003)

    CAS  Article  Google Scholar 

  17. Moore, T., Zhang, Y., Fenley, M. O. & Li, H. Molecular basis of box C/D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure 12, 807–818 (2004)

    CAS  Article  Google Scholar 

  18. Tran, E., Zhang, X., Lackey, L. & Maxwell, E. S. Conserved spacing between the box C/D and C′/D′ RNPs of the archaeal box C/D sRNP complex is required for efficient 2′-O-methylation of target RNAs. RNA 11, 285–293 (2005)

    CAS  Article  Google Scholar 

  19. Hardin, J. W. & Batey, R. T. The bipartite architecture of the sRNA in an archaeal box C/D complex is a primary determinant of specificity. Nucleic Acids Res. 34, 5039–5051 (2006)

    CAS  Article  Google Scholar 

  20. Omer, A. D., Zago, M., Chang, A. & Dennis, P. P. Probing the structure and function of an archaeal C/D-box methylation guide sRNA. RNA 12, 1708–1720 (2006)

    CAS  Article  Google Scholar 

  21. Zhang, X. et al. The coiled-coil domain of the Nop56/58 core protein is dispensable for sRNP assembly but is critical for archaeal box C/D sRNP-guided nucleotide methylation. RNA 12, 1092–1103 (2006)

    CAS  Article  Google Scholar 

  22. Oruganti, S. et al. Alternative conformations of the archaeal Nop56/58-fibrillarin complex imply flexibility in box C/D RNPs. J. Mol. Biol. 371, 1141–1150 (2007)

    CAS  Article  Google Scholar 

  23. Ye, K. et al. Structural organization of box C/D RNA-guided RNA methyltransferase. Proc. Natl Acad. Sci. USA 106, 13808–13813 (2009)

    ADS  CAS  Article  Google Scholar 

  24. Bleichert, F. et al. A dimeric structure for archaeal box C/D small ribonucleoproteins. Science 325, 1384–1387 (2009)

    ADS  CAS  Article  Google Scholar 

  25. Xue, S. et al. Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle. Mol. Cell 39, 939–949 (2010)

    CAS  Article  Google Scholar 

  26. Klein, D. J., Schmeing, T. M., Moore, P. B. & Steitz, T. A. The kink-turn: a new RNA secondary structure motif. EMBO J. 20, 4214–4221 (2001)

    CAS  Article  Google Scholar 

  27. Watkins, N. J., Dickmanns, A. & Luhrmann, R. Conserved stem II of the box C/D motif is essential for nucleolar localization and is required, along with the 15.5K protein, for the hierarchical assembly of the box C/D snoRNP. Mol. Cell. Biol. 22, 8342–8352 (2002)

    CAS  Article  Google Scholar 

  28. Chen, C. L., Perasso, R., Qu, L. H. & Amar, L. Exploration of pairing constraints identifies a 9 base-pair core within box C/D snoRNA-rRNA duplexes. J. Mol. Biol. 369, 771–783 (2007)

    CAS  Article  Google Scholar 

  29. Appel, C. D. & Maxwell, E. S. Structural features of the guide:target RNA duplex required for archaeal box C/D sRNA-guided nucleotide 2′-O-methylation. RNA 13, 899–911 (2007)

    CAS  Article  Google Scholar 

  30. DeLano, W. L. The PyMOL User’s Manual (Delano Scientific, 2002)

    Google Scholar 

  31. Price, S. R., Ito, N., Oubridge, C., Avis, J. M. & Nagai, K. Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallographic studies. J. Mol. Biol. 249, 398–408 (1995)

    CAS  Article  Google Scholar 

  32. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    CAS  Article  Google Scholar 

  33. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)

    CAS  Article  Google Scholar 

  34. Vagin, A. A. & Teplyakov, A. MOLREP: an automated program for molecular replacement. J. Appl. Cryst. 30, 1022–1025 (1997)

    CAS  Article  Google Scholar 

  35. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

  36. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    CAS  Article  Google Scholar 

  37. Murshudov, G. N., Vagin, A. A., Lebedev, A., Wilson, K. S. & Dodson, E. J. Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr. D 55, 247–255 (1999)

    CAS  Article  Google Scholar 

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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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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.

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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).

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