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An asymmetric interface between the regulatory and core particles of the proteasome

Nature Structural & Molecular Biology volume 18, pages 1259–1267 (2011)Cite this article

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Abstract

The Saccharomyces cerevisiae proteasome comprises a 19-subunit regulatory particle and a 28-subunit core particle. To be degraded, substrates must cross the core particle–regulatory particle interface, a site for complex conformational changes and regulatory events. This interface includes two aligned heteromeric rings, one formed by the six ATPase (Rpt) subunits of the regulatory particle and the other by the seven α subunits of the core particle. The Rpt C termini bind to intersubunit cavities in the α-ring, thus directing core particle gating and proteasome assembly. We mapped the Rpt C termini to the α subunit pockets, using a cross-linking approach that revealed an unexpected asymmetry: one side of the ring shows 1:1 contacts of Rpt2-α4, Rpt6-α3 and Rpt3-α2, whereas on the opposite side, the Rpt1, Rpt4 and Rpt5 tails each cross-link to multiple α pockets. Rpt–core particle cross-links are all sensitive to nucleotides, implying that ATP hydrolysis drives dynamic alterations at the core particle–regulatory particle interface.

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Figure 1: Structural basis for the cross-linking strategy.
Figure 2: Identification of two α-Rpt subunit pairs by cysteine cross-linking.
Figure 3: Identification of the α4-Rpt2 pair.
Figure 4: Identification of the α3-Rpt6 and α2-Rpt3 pairs.
Figure 5: Identification of cross-links for α5-α6 and α6-α7 pockets.
Figure 6: Model of the base–core particle complex.
Figure 7: Effect of nucleotides on cross-linking between α and Rpt subunits.
Figure 8: The α subunit N-terminal tails and the Rpt proteins proposed to direct their movements.

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Acknowledgements

We thank W. Tansey (Vanderbilt University Medical Center) and C. Mann (Commissariat à l'énergie atomique et aux énergies alternatives (CEA)/Saclay) for antibodies, B.-H. Lee for helpful discussions, A. Matouschek for comments on the manuscript and W. Baumeister for permission to reproduce Figure 6D. Funding was provided by US National Institutes of Health grants to D.F. (R37GM43601), C.P.H. (R01 GM59135) and S.G. (GM67945). S.P. was supported by a fellowship from the Charles A. King Trust and M.J.L. by the American Health Assistance Foundation.

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  1. Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA

    Geng Tian, Soyeon Park, Min Jae Lee, Bettina Huck, Fiona McAllister, Steven P Gygi & Daniel Finley

  2. Department of Applied Chemistry, Kyung Hee University, Gyeonggi-do, Republic of Korea

    Min Jae Lee

  3. Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA

    Christopher P Hill

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Contributions

G.T., S.P., C.P.H. and D.F. contributed to the conception of this project. G.T., S.P. and B.H. contributed to strain construction and genetic analysis. G.T, S.P. and M.J.L. conducted cross-linking studies. F.M. and S.P.G. carried out mass spectrometry on cross-linked samples. G.T., C.P.H. and D.F. were largely responsible for the manuscript.

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Correspondence to Daniel Finley.

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Tian, G., Park, S., Lee, M. et al. An asymmetric interface between the regulatory and core particles of the proteasome. Nat Struct Mol Biol 18, 1259–1267 (2011). https://doi.org/10.1038/nsmb.2147

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