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Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis

Abstract

The spliceosome is a dynamic macromolecular machine that assembles on pre-messenger RNA substrates and catalyses the excision of non-coding intervening sequences (introns)1,2,3. Four of the five major components of the spliceosome, U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), contain seven Sm proteins (SmB/B′, SmD1, SmD2, SmD3, SmE, SmF and SmG) in common4,5. Following export of the U1, U2, U4 and U5 snRNAs to the cytoplasm6,7, the seven Sm proteins, chaperoned by the survival of motor neurons (SMN) complex, assemble around a single-stranded, U-rich sequence called the Sm site in each small nuclear RNA (snRNA), to form the core domain of the respective snRNP particle8,9. Core domain formation is a prerequisite for re-import into the nucleus10, where these snRNPs mature via addition of their particle-specific proteins. Here we present a crystal structure of the U4 snRNP core domain at 3.6 Å resolution, detailing how the Sm site heptad (AUUUUUG) binds inside the central hole of the heptameric ring of Sm proteins, interacting one-to-one with SmE–SmG–SmD3–SmB–SmD1–SmD2–SmF. An irregular backbone conformation of the Sm site sequence combined with the asymmetric structure of the heteromeric protein ring allows each base to interact in a distinct manner with four key residues at equivalent positions in the L3 and L5 loops of the Sm fold. A comparison of this structure with the U1 snRNP at 5.5 Å resolution11,12 reveals snRNA-dependent structural changes outside the Sm fold, which may facilitate the binding of particle-specific proteins that are crucial to biogenesis of spliceosomal snRNPs.

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Figure 1: Overall structure of the U4 snRNP core domain.
Figure 2: The Sm site RNA binds asymmetrically in the central hole of the heptamer ring.
Figure 3: Interactions between the U4 Sm site heptad nucleotides and the Sm proteins.
Figure 4: snRNA-dependent structural changes of the U1 and U4 core domains.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the U4 snRNP core domain have been deposited in the PDB data bank under accession numbers 2Y9A, 2Y9B, 2Y9C and 2Y9D.

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Acknowledgements

This work was supported by the Medical Research Council of the UK and a HFSP grant. A.K.W.L. was supported by the Overseas Research Students Awards Scheme, Canada-Cambridge Commonwealth studentship, a postgraduate scholarship from NSERC and a Junior Research Fellowship from Sidney Sussex College, Cambridge University. We thank the European Synchrotron Radiation Facility and Daresbury beamline staff for their support. We thank M. Jinek, M. Kampmann and Y. Kondo for their help with crystallization. We also thank C. Kambach, J. Avis, R. Young, S. Walke and H. Teo for laying the foundation of this project, C. Oubridge and D. Pomeranz Krummel for sharing Sm proteins and providing help and advice throughout the project, and P. Zwart for advice on twinning.

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A.K.W.L. and K.N. designed the constructs. A.K.W.L. crystallized the core domain, collected data and solved the structure in P6122. J.L. identified twinning and refined the structure in P31. All three authors wrote the paper.

Corresponding authors

Correspondence to Kiyoshi Nagai or Jade Li.

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The authors declare no competing financial interests.

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Leung, A., Nagai, K. & Li, J. Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis. Nature 473, 536–539 (2011). https://doi.org/10.1038/nature09956

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