Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Crystal structure of an H/ACA box ribonucleoprotein particle

Abstract

H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. They also participate in eukaryotic ribosomal RNA processing and are a component of vertebrate telomerases. Here we report the crystal structure, at 2.3 Å resolution, of an entire archaeal H/ACA RNP consisting of proteins Cbf5, Nop10, Gar1 and L7ae, and a single-hairpin H/ACA RNA, revealing a modular organization of the complex. The RNA upper stem is bound to a composite surface formed by L7ae, Nop10 and Cbf5, and the RNA lower stem and ACA signature motif are bound to the PUA domain of Cbf5, thereby positioning middle guide sequences so that they are primed to pair with substrate RNA. Furthermore, Gar1 may regulate substrate loading and release. The structure rationalizes the consensus structure of H/ACA RNAs, suggests a functional role of each protein, and provides a framework for understanding the mechanism of RNA-guided pseudouridylation, as well as various cellular functions of H/ACA RNP.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Structure of H/ACA RNP.
Figure 2: PUA recognition of the P1 stem and the ACA motif.
Figure 3: Recognition of the P2 stem and pseudouridylation pocket.
Figure 4: Proposed mechanism of RNA-guided pseudouridylation.

References

  1. 1

    Ofengand, J. Ribosomal RNA pseudouridines and pseudouridine synthases. FEBS Lett. 514, 17–25 (2002)

    CAS  Article  Google Scholar 

  2. 2

    Kiss, T. Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109, 145–148 (2002)

    CAS  Article  Google Scholar 

  3. 3

    Meier, U. T. The many facets of H/ACA ribonucleoproteins. Chromosoma 114, 1–14 (2005)

    CAS  Article  Google Scholar 

  4. 4

    Torchet, C. et al. The complete set of H/ACA snoRNAs that guide rRNA pseudouridylations in Saccharomyces cerevisiae. RNA 11, 928–938 (2005)

    CAS  Article  Google Scholar 

  5. 5

    Lestrade, L. & Weber, M. J. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res. 34, D158–D162 (2006)

    CAS  Article  Google Scholar 

  6. 6

    Ganot, P., Bortolin, M. L. & Kiss, T. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89, 799–809 (1997)

    CAS  Article  Google Scholar 

  7. 7

    Ni, J., Tien, A. L. & Fournier, M. J. Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell 89, 565–573 (1997)

    CAS  Article  Google Scholar 

  8. 8

    Balakin, A. G., Smith, L. & Fournier, M. J. The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell 86, 823–834 (1996)

    CAS  Article  Google Scholar 

  9. 9

    Ganot, P., Caizergues-Ferrer, M. & Kiss, T. The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev. 11, 941–956 (1997)

    CAS  Article  Google Scholar 

  10. 10

    Rozhdestvensky, T. S. et al. Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res. 31, 869–877 (2003)

    CAS  Article  Google Scholar 

  11. 11

    Morrissey, J. P. & Tollervey, D. Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis. Mol. Cell. Biol. 13, 2469–2477 (1993)

    CAS  Article  Google Scholar 

  12. 12

    Atzorn, V., Fragapane, P. & Kiss, T. U17/snR30 is a ubiquitous snoRNA with two conserved sequence motifs essential for 18S rRNA production. Mol. Cell. Biol. 24, 1769–1778 (2004)

    CAS  Article  Google Scholar 

  13. 13

    Mitchell, J. R., Cheng, J. & Collins, K. A box H/ACA small nucleolar RNA-like domain at the human telomerase RNA 3′ end. Mol. Cell. Biol. 19, 567–576 (1999)

    CAS  Article  Google Scholar 

  14. 14

    Girard, J. P. et al. GAR1 is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast. EMBO J. 11, 673–682 (1992)

    CAS  Article  Google Scholar 

  15. 15

    Bousquet-Antonelli, C., Henry, Y., G'elugne, J. P., Caizergues-Ferrer, M. & Kiss, T. A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs. EMBO J. 16, 4770–4776 (1997)

    CAS  Article  Google Scholar 

  16. 16

    Lafontaine, D. L., Bousquet-Antonelli, C., Henry, Y., Caizergues-Ferrer, M. & Tollervey, D. The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Genes Dev. 12, 527–537 (1998)

    CAS  Article  Google Scholar 

  17. 17

    Watkins, N. J. et al. Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ACA-motif snoRNPs and constitute a common bipartite structure. RNA 4, 1549–1568 (1998)

    CAS  Article  Google Scholar 

  18. 18

    Henras, A. et al. Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs. EMBO J. 17, 7078–7090 (1998)

    CAS  Article  Google Scholar 

  19. 19

    Baker, D. L. et al. RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP. Genes Dev. 19, 1238–1248 (2005)

    CAS  Article  Google Scholar 

  20. 20

    Charpentier, B., Muller, S. & Branlant, C. Reconstitution of archaeal H/ACA small ribonucleoprotein complexes active in pseudouridylation. Nucleic Acids Res. 33, 3133–3144 (2005)

    CAS  Article  Google Scholar 

  21. 21

    Wang, C. & Meier, U. T. Architecture and assembly of mammalian H/ACA small nucleolar and telomerase ribonucleoproteins. EMBO J. 23, 1857–1867 (2004)

    CAS  Article  Google Scholar 

  22. 22

    Henras, A. K., Capeyrou, R., Henry, Y. & Caizergues-Ferrer, M. Cbf5p, the putative pseudouridine synthase of H/ACA-type snoRNPs, can form a complex with Gar1p and Nop10p in absence of Nhp2p and box H/ACA snoRNAs. RNA 10, 1704–1712 (2004)

    CAS  Article  Google Scholar 

  23. 23

    Rashid, R. et al. Crystal structure of a Cbf5–Nop10–Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita. Mol. Cell 21, 249–260 (2006)

    CAS  Article  Google Scholar 

  24. 24

    Hamma, T., Reichow, S. L., Varani, G. & Ferre-D'Amare, A. R. The Cbf5–Nop10 complex is a molecular bracket that organizes box H/ACA RNPs. Nature Struct. Mol. Biol. 12, 1101–1107 (2005)

    CAS  Article  Google Scholar 

  25. 25

    Manival, X. et al. Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5–aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity. Nucleic Acids Res. 34, 826–839 (2006)

    CAS  Article  Google Scholar 

  26. 26

    Girard, J. P., Bagni, C., Caizergues-Ferrer, M., Amalric, F. & Lapeyre, B. Identification of a segment of the small nucleolar ribonucleoprotein-associated protein GAR1 that is sufficient for nucleolar accumulation. J. Biol. Chem. 269, 18499–18506 (1994)

    CAS  PubMed  Google Scholar 

  27. 27

    Ishitani, R. et al. Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell 113, 383–394 (2003)

    CAS  Article  Google Scholar 

  28. 28

    Liang, X. H. et al. A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modification. RNA 11, 619–645 (2005)

    CAS  Article  Google Scholar 

  29. 29

    Russell, A. G., Schnare, M. N. & Gray, M. W. Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis. RNA 10, 1034–1046 (2004)

    CAS  Article  Google Scholar 

  30. 30

    Heiss, N. S. et al. X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions. Nature Genet. 19, 32–38 (1998)

    CAS  Article  Google Scholar 

  31. 31

    Marrone, A., Walne, A. & Dokal, I. Dyskeratosis congenita: telomerase, telomeres and anticipation. Curr. Opin. Genet. Dev. 15, 249–257 (2005)

    CAS  Article  Google Scholar 

  32. 32

    Hoang, C. & Ferre-D'Amare, A. R. Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. Cell 107, 929–939 (2001)

    CAS  Article  Google Scholar 

  33. 33

    Pan, H., Agarwalla, S., Moustakas, D. T., Finer-Moore, J. & Stroud, R. M. Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit. Proc. Natl Acad. Sci. USA 100, 12648–12653 (2003)

    ADS  CAS  Article  Google Scholar 

  34. 34

    DeLano, W. L. The PyMOL User's Manual (Delano Scientific, San Carlos, California, 2002)

    Google Scholar 

Download references

Acknowledgements

We are grateful to D. J. Patel for his steady interest and encouragement in this project. We thank D. Patel and A. Serganov for critically reading the paper, and J. Duan, Y. Kang and W. Wang for assistance and discussion. We thank N. Shimizu and M. Kawamoto for help at SPring-8 beamline BL41XU. This research is funded by the Chinese Ministry of Science and Technology. Author Contributions L.L. was responsible for biochemical and crystallization experiments; K.Y. determined the structure and wrote the paper. Both authors designed experiments and discussed results.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Keqiong Ye.

Ethics declarations

Competing interests

Coordinates and structure factors have been deposited in the Protein Data Bank under the accession code 2HVY. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Data

This file contains Supplementary discussion, methods, references, Table S1 and Figure S1–S7. (PDF 1165 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Li, L., Ye, K. Crystal structure of an H/ACA box ribonucleoprotein particle. Nature 443, 302–307 (2006). https://doi.org/10.1038/nature05151

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing