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Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution

Nature volume 458, pages 475–480 (2009)Cite this article

Abstract

Human spliceosomal U1 small nuclear ribonucleoprotein particles (snRNPs), which consist of U1 small nuclear RNA and ten proteins, recognize the 5′ splice site within precursor messenger RNAs and initiate the assembly of the spliceosome for intron excision. An electron density map of the functional core of U1 snRNP at 5.5 Å resolution has enabled us to build the RNA and, in conjunction with site-specific labelling of individual proteins, to place the seven Sm proteins, U1-C and U1-70K into the map. Here we present the detailed structure of a spliceosomal snRNP, revealing a hierarchical network of intricate interactions between subunits. A striking feature is the amino (N)-terminal polypeptide of U1-70K, which extends over a distance of 180 Å from its RNA binding domain, wraps around the core domain consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5′-splice-site recognition. The structure of U1 snRNP provides insights into U1 snRNP assembly and suggests a possible mechanism of 5′-splice-site recognition.

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Figure 1: Overall fold of U1 snRNA and the U1 snRNP core domain containing the seven Sm proteins.
Figure 2: Structure of the U1 snRNP core domain.
Figure 3: A mechanism of 5′-splice-site recognition.
Figure 4: Interaction of U1-70K with SL1 of U1 snRNA, the core domain and U1-C.
Figure 5: Model of the complete human U1 snRNP.

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Protein Data Bank

Data deposits

Coordinates of the protein α-carbon and the RNA phosphorus atoms have been submitted, together with structure factors, to the Protein Data Bank under accession number 3CW1.

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Acknowledgements

We are grateful to T. Jessen, C. Kambach, J. Avis, R. Young, Y. Muto, S. Walke and T. Ignjatovic for expressing U1 snRNP proteins and laying the foundation of this project. We thank Swiss Light Source, Daresbury and European Synchrotron Radiation Facility beamline staff, particularly C. Schulze-Briese, T. Tomizaki and A. Pauluhn at the Swiss Light Source, for their support; V. Ramakrishnan, A. Newman, A. Andreeva, A. Murzin and C. Vonrhein for discussions; the current members of the Nagai group for help; S. Sengupta for support; and H. Stark for making the cryo-electron microscopy structure available. This project has been funded by the Medical Research Council and the Human Frontier Science Program (HFSP). D.A.P.K. was a recipient of a HFSP long-term fellowship. A.K.W.L was supported by the National Science and Engineering Research Council of Canada, the ORS Fund, the Cambridge Commonwealth Trust and Sidney Sussex College Junior Research Fellowship.

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  1. Daniel A. Pomeranz Krummel & Adelaine K. W. Leung

    Present address: Present addresses: Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA (D.A.P.K.); Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA (A.K.W.L.).,

  2. Daniel A. Pomeranz Krummel and Chris Oubridge: These authors contributed equally to this work.

Authors and Affiliations

  1. MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK ,

    Daniel A. Pomeranz Krummel, Chris Oubridge, Adelaine K. W. Leung, Jade Li & Kiyoshi Nagai

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Pomeranz Krummel, D., Oubridge, C., Leung, A. et al. Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution. Nature 458, 475–480 (2009). https://doi.org/10.1038/nature07851

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