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Crystal structure of an H/ACA box ribonucleoprotein particle


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.

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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.


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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.

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Correspondence to Keqiong Ye.

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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 The authors declare no competing financial interests.

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

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

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