Crossref journal-article
Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences (341)
Abstract

Significance The proteasome holoenzyme is an ATP-dependent protease in eukaryotes that degrades ubiquitylated substrates. It is involved in numerous important biological processes, such as cell division, differentiation, innate immunity, adaptive immunity, regulation of gene expression, and response to proteotoxic stress. Using cryoelectron microscopy, we have examined multiple conformational states of the human proteasome at medium to high resolution. Our results reveal that the substrate-conducting channel in the core particle is transiently opened and accompanied by dynamic changes in structure of the particle. These observations provide new insights into how the proteasome recognizes ubiquitylated substrates and translocates them through a channel and gate to degradation sites in the core particle.

Bibliography

Chen, S., Wu, J., Lu, Y., Ma, Y.-B., Lee, B.-H., Yu, Z., Ouyang, Q., Finley, D. J., Kirschner, M. W., & Mao, Y. (2016). Structural basis for dynamic regulation of the human 26S proteasome. Proceedings of the National Academy of Sciences, 113(46), 12991–12996.

Authors 10
  1. Shuobing Chen (first)
  2. Jiayi Wu (additional)
  3. Ying Lu (additional)
  4. Yong-Bei Ma (additional)
  5. Byung-Hoon Lee (additional)
  6. Zhou Yu (additional)
  7. Qi Ouyang (additional)
  8. Daniel J. Finley (additional)
  9. Marc W. Kirschner (additional)
  10. Youdong Mao (additional)
References 50 Referenced 161
  1. D Finley, X Chen, KJ Walters, Gates, channels, and switches: Elements of the proteasome machine. Trends Biochem Sci 41, 77–93 (2016). (10.1016/j.tibs.2015.10.009) / Trends Biochem Sci / Gates, channels, and switches: Elements of the proteasome machine by Finley D (2016)
  2. Jr RJ Tomko, M Hochstrasser, Molecular architecture and assembly of the eukaryotic proteasome. Annu Rev Biochem 82, 415–445 (2013). (10.1146/annurev-biochem-060410-150257) / Annu Rev Biochem / Molecular architecture and assembly of the eukaryotic proteasome by Tomko RJ (2013)
  3. E Kish-Trier, CP Hill, Structural biology of the proteasome. Annu Rev Biophys 42, 29–49 (2013). (10.1146/annurev-biophys-083012-130417) / Annu Rev Biophys / Structural biology of the proteasome by Kish-Trier E (2013)
  4. D Finley, Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu Rev Biochem 78, 477–513 (2009). (10.1146/annurev.biochem.78.081507.101607) / Annu Rev Biochem / Recognition and processing of ubiquitin-protein conjugates by the proteasome by Finley D (2009)
  5. W Harshbarger, C Miller, C Diedrich, J Sacchettini, Crystal structure of the human 20S proteasome in complex with carfilzomib. Structure 23, 418–424 (2015). (10.1016/j.str.2014.11.017) / Structure / Crystal structure of the human 20S proteasome in complex with carfilzomib by Harshbarger W (2015)
  6. EM Huber, M Groll, Inhibitors for the immuno- and constitutive proteasome: Current and future trends in drug development. Angew Chem Int Ed Engl 51, 8708–8720 (2012). (10.1002/anie.201201616) / Angew Chem Int Ed Engl / Inhibitors for the immuno- and constitutive proteasome: Current and future trends in drug development by Huber EM (2012)
  7. F Beck, , Near-atomic resolution structural model of the yeast 26S proteasome. Proc Natl Acad Sci USA 109, 14870–14875 (2012). (10.1073/pnas.1213333109) / Proc Natl Acad Sci USA / Near-atomic resolution structural model of the yeast 26S proteasome by Beck F (2012)
  8. K Lasker, , Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci USA 109, 1380–1387 (2012). (10.1073/pnas.1120559109) / Proc Natl Acad Sci USA / Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach by Lasker K (2012)
  9. GC Lander, , Complete subunit architecture of the proteasome regulatory particle. Nature 482, 186–191 (2012). (10.1038/nature10774) / Nature / Complete subunit architecture of the proteasome regulatory particle by Lander GC (2012)
  10. PC da Fonseca, J He, EP Morris, Molecular model of the human 26S proteasome. Mol Cell 46, 54–66 (2012). (10.1016/j.molcel.2012.03.026) / Mol Cell / Molecular model of the human 26S proteasome by da Fonseca PC (2012)
  11. J Löwe, , Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution. Science 268, 533–539 (1995). (10.1126/science.7725097) / Science / Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution by Löwe J (1995)
  12. M Groll, , Structure of 20S proteasome from yeast at 2.4Å resolution. Nature 386, 463–471 (1997). (10.1038/386463a0) / Nature / Structure of 20S proteasome from yeast at 2.4Å resolution by Groll M (1997)
  13. M Unno, , The structure of the mammalian 20S proteasome at 2.75 Å resolution. Structure 10, 609–618 (2002). (10.1016/S0969-2126(02)00748-7) / Structure / The structure of the mammalian 20S proteasome at 2.75 Å resolution by Unno M (2002)
  14. GR Pathare, , The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together. Proc Natl Acad Sci USA 109, 149–154 (2012). (10.1073/pnas.1117648108) / Proc Natl Acad Sci USA / The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together by Pathare GR (2012)
  15. GR Pathare, , Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11. Proc Natl Acad Sci USA 111, 2984–2989 (2014). (10.1073/pnas.1400546111) / Proc Natl Acad Sci USA / Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11 by Pathare GR (2014)
  16. C Riedinger, , Structure of Rpn10 and its interactions with polyubiquitin chains and the proteasome subunit Rpn12. J Biol Chem 285, 33992–34003 (2010). (10.1074/jbc.M110.134510) / J Biol Chem / Structure of Rpn10 and its interactions with polyubiquitin chains and the proteasome subunit Rpn12 by Riedinger C (2010)
  17. Q Wang, P Young, KJ Walters, Structure of S5a bound to monoubiquitin provides a model for polyubiquitin recognition. J Mol Biol 348, 727–739 (2005). (10.1016/j.jmb.2005.03.007) / J Mol Biol / Structure of S5a bound to monoubiquitin provides a model for polyubiquitin recognition by Wang Q (2005)
  18. EJ Worden, C Padovani, A Martin, Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Nat Struct Mol Biol 21, 220–227 (2014). (10.1038/nsmb.2771) / Nat Struct Mol Biol / Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation by Worden EJ (2014)
  19. N Zhang, , Structure of the S5a:K48-linked diubiquitin complex and its interactions with Rpn13. Mol Cell 35, 280–290 (2009). (10.1016/j.molcel.2009.06.010) / Mol Cell / Structure of the S5a:K48-linked diubiquitin complex and its interactions with Rpn13 by Zhang N (2009)
  20. CM Dambacher, EJ Worden, MA Herzik, A Martin, GC Lander, Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition. eLife 5, e13027 (2016). (10.7554/eLife.13027) / eLife / Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition by Dambacher CM (2016)
  21. J Boehringer, , Structural and functional characterization of Rpn12 identifies residues required for Rpn10 proteasome incorporation. Biochem J 448, 55–65 (2012). (10.1042/BJ20120542) / Biochem J / Structural and functional characterization of Rpn12 identifies residues required for Rpn10 proteasome incorporation by Boehringer J (2012)
  22. J He, , The structure of the 26S proteasome subunit Rpn2 reveals its PC repeat domain as a closed toroid of two concentric α-helical rings. Structure 20, 513–521 (2012). (10.1016/j.str.2011.12.015) / Structure / The structure of the 26S proteasome subunit Rpn2 reveals its PC repeat domain as a closed toroid of two concentric α-helical rings by He J (2012)
  23. F Zhang, , Structural insights into the regulatory particle of the proteasome from Methanocaldococcus jannaschii. Mol Cell 34, 473–484 (2009). (10.1016/j.molcel.2009.04.021) / Mol Cell / Structural insights into the regulatory particle of the proteasome from Methanocaldococcus jannaschii by Zhang F (2009)
  24. F Zhang, , Mechanism of substrate unfolding and translocation by the regulatory particle of the proteasome from Methanocaldococcus jannaschii. Mol Cell 34, 485–496 (2009). (10.1016/j.molcel.2009.04.022) / Mol Cell / Mechanism of substrate unfolding and translocation by the regulatory particle of the proteasome from Methanocaldococcus jannaschii by Zhang F (2009)
  25. B Luan, , Structure of an endogenous yeast 26S proteasome reveals two major conformational states. Proc Natl Acad Sci USA 113, 2642–2647 (2016). (10.1073/pnas.1601561113) / Proc Natl Acad Sci USA / Structure of an endogenous yeast 26S proteasome reveals two major conformational states by Luan B (2016)
  26. ME Matyskiela, GC Lander, A Martin, Conformational switching of the 26S proteasome enables substrate degradation. Nat Struct Mol Biol 20, 781–788 (2013). (10.1038/nsmb.2616) / Nat Struct Mol Biol / Conformational switching of the 26S proteasome enables substrate degradation by Matyskiela ME (2013)
  27. P Śledź, , Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation. Proc Natl Acad Sci USA 110, 7264–7269 (2013). (10.1073/pnas.1305782110) / Proc Natl Acad Sci USA / Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation by Śledź P (2013)
  28. P Unverdorben, , Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome. Proc Natl Acad Sci USA 111, 5544–5549 (2014). (10.1073/pnas.1403409111) / Proc Natl Acad Sci USA / Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome by Unverdorben P (2014)
  29. E Estrin, JR Lopez-Blanco, P Chacón, A Martin, Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid. Structure 21, 1624–1635 (2013). (10.1016/j.str.2013.06.023) / Structure / Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid by Estrin E (2013)
  30. X Wang, , Mass spectrometric characterization of the affinity-purified human 26S proteasome complex. Biochemistry 46, 3553–3565 (2007). (10.1021/bi061994u) / Biochemistry / Mass spectrometric characterization of the affinity-purified human 26S proteasome complex by Wang X (2007)
  31. SH Scheres, , Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat Methods 4, 27–29 (2007). (10.1038/nmeth992) / Nat Methods / Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization by Scheres SH (2007)
  32. SH Scheres, A Bayesian view on cryo-EM structure determination. J Mol Biol 415, 406–418 (2012). (10.1016/j.jmb.2011.11.010) / J Mol Biol / A Bayesian view on cryo-EM structure determination by Scheres SH (2012)
  33. FG Whitby, , Structural basis for the activation of 20S proteasomes by 11S regulators. Nature 408, 115–120 (2000). (10.1038/35040607) / Nature / Structural basis for the activation of 20S proteasomes by 11S regulators by Whitby FG (2000)
  34. RT Sauer, TA Baker, AAA+ proteases: ATP-fueled machines of protein destruction. Annu Rev Biochem 80, 587–612 (2011). (10.1146/annurev-biochem-060408-172623) / Annu Rev Biochem / AAA+ proteases: ATP-fueled machines of protein destruction by Sauer RT (2011)
  35. T Ogura, AJ Wilkinson, AAA+ superfamily ATPases: Common structure–diverse function. Genes Cells 6, 575–597 (2001). (10.1046/j.1365-2443.2001.00447.x) / Genes Cells / AAA+ superfamily ATPases: Common structure–diverse function by Ogura T (2001)
  36. R Beckwith, E Estrin, EJ Worden, A Martin, Reconstitution of the 26S proteasome reveals functional asymmetries in its AAA+ unfoldase. Nat Struct Mol Biol 20, 1164–1172 (2013). (10.1038/nsmb.2659) / Nat Struct Mol Biol / Reconstitution of the 26S proteasome reveals functional asymmetries in its AAA+ unfoldase by Beckwith R (2013)
  37. SE Glynn, A Martin, AR Nager, TA Baker, RT Sauer, Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Cell 139, 744–756 (2009). (10.1016/j.cell.2009.09.034) / Cell / Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine by Glynn SE (2009)
  38. O Iosefson, AR Nager, TA Baker, RT Sauer, Coordinated gripping of substrate by subunits of a AAA+ proteolytic machine. Nat Chem Biol 11, 201–206 (2015). (10.1038/nchembio.1732) / Nat Chem Biol / Coordinated gripping of substrate by subunits of a AAA+ proteolytic machine by Iosefson O (2015)
  39. X Zhang, DB Wigley, The ‘glutamate switch’ provides a link between ATPase activity and ligand binding in AAA+ proteins. Nat Struct Mol Biol 15, 1223–1227 (2008). (10.1038/nsmb.1501) / Nat Struct Mol Biol / The ‘glutamate switch’ provides a link between ATPase activity and ligand binding in AAA+ proteins by Zhang X (2008)
  40. G Tian, , An asymmetric interface between the regulatory and core particles of the proteasome. Nat Struct Mol Biol 18, 1259–1267 (2011). (10.1038/nsmb.2147) / Nat Struct Mol Biol / An asymmetric interface between the regulatory and core particles of the proteasome by Tian G (2011)
  41. BM Stadtmueller, , Structural models for interactions between the 20S proteasome and its PAN/19S activators. J Biol Chem 285, 13–17 (2010). (10.1074/jbc.C109.070425) / J Biol Chem / Structural models for interactions between the 20S proteasome and its PAN/19S activators by Stadtmueller BM (2010)
  42. YC Kim, GN DeMartino, C termini of proteasomal ATPases play nonequivalent roles in cellular assembly of mammalian 26 S proteasome. J Biol Chem 286, 26652–26666 (2011). (10.1074/jbc.M111.246793) / J Biol Chem / C termini of proteasomal ATPases play nonequivalent roles in cellular assembly of mammalian 26 S proteasome by Kim YC (2011)
  43. SH Lee, JH Moon, SK Yoon, JB Yoon, Stable incorporation of ATPase subunits into 19 S regulatory particle of human proteasome requires nucleotide binding and C-terminal tails. J Biol Chem 287, 9269–9279 (2012). (10.1074/jbc.M111.316208) / J Biol Chem / Stable incorporation of ATPase subunits into 19 S regulatory particle of human proteasome requires nucleotide binding and C-terminal tails by Lee SH (2012)
  44. M Groll, , A gated channel into the proteasome core particle. Nat Struct Biol 7, 1062–1067 (2000). (10.1038/80992) / Nat Struct Biol / A gated channel into the proteasome core particle by Groll M (2000)
  45. J Erales, MA Hoyt, F Troll, P Coffino, Functional asymmetries of proteasome translocase pore. J Biol Chem 287, 18535–18543 (2012). (10.1074/jbc.M112.357327) / J Biol Chem / Functional asymmetries of proteasome translocase pore by Erales J (2012)
  46. A Peth, N Kukushkin, M Bossé, AL Goldberg, Ubiquitinated proteins activate the proteasomal ATPases by binding to Usp14 or Uch37 homologs. J Biol Chem 288, 7781–7790 (2013). (10.1074/jbc.M112.441907) / J Biol Chem / Ubiquitinated proteins activate the proteasomal ATPases by binding to Usp14 or Uch37 homologs by Peth A (2013)
  47. A Schweitzer, , Structure of the human 26S proteasome at a resolution of 3.9 Å. Proc Natl Acad Sci USA 113, 7816–7821 (2016). (10.1073/pnas.1608050113) / Proc Natl Acad Sci USA / Structure of the human 26S proteasome at a resolution of 3.9 Å by Schweitzer A (2016)
  48. X Huang, B Luan, J Wu, Y Shi, An atomic structure of the human 26S proteasome. Nat Struct Mol Biol 23, 778–785 (2016). (10.1038/nsmb.3273) / Nat Struct Mol Biol / An atomic structure of the human 26S proteasome by Huang X (2016)
  49. J Wu Unsupervised single-particle deep classification via statistical manifold learning. arXiv:1604.04539. (2016).
  50. OS Smart, JG Neduvelil, X Wang, BA Wallace, MS Sansom, HOLE: A program for the analysis of the pore dimensions of ion channel structural models. J Mol Graph 14, 354–360, 376 (1996). (10.1016/S0263-7855(97)00009-X) / J Mol Graph / HOLE: A program for the analysis of the pore dimensions of ion channel structural models by Smart OS (1996)
Dates
Type When
Created 8 years, 10 months ago (Oct. 21, 2016, 11:40 p.m.)
Deposited 3 years, 2 months ago (June 7, 2022, 11:03 a.m.)
Indexed 1 month ago (July 27, 2025, 3:51 a.m.)
Issued 8 years, 10 months ago (Oct. 21, 2016)
Published 8 years, 10 months ago (Oct. 21, 2016)
Published Online 8 years, 10 months ago (Oct. 21, 2016)
Published Print 8 years, 9 months ago (Nov. 15, 2016)
Funders 3
  1. HHS | NIH | National Institute of General Medical Sciences 10.13039/100000057 National Institute of General Medical Sciences

    Region: Americas

    gov (National government)

    Labels2
    1. U.S. National Institute of General Medical Sciences
    2. NIGMS
    Awards1
    1. GM026875
  2. National Natural Science Foundation of China 10.13039/501100001809

    Region: Asia

    gov (National government)

    Labels11
    1. Chinese National Science Foundation
    2. Natural Science Foundation of China
    3. National Science Foundation of China
    4. NNSF of China
    5. NSF of China
    6. 国家自然科学基金委员会
    7. National Nature Science Foundation of China
    8. Guójiā Zìrán Kēxué Jījīn Wěiyuánhuì
    9. NSFC
    10. NNSF
    11. NNSFC
    Awards1
    1. 91530321
  3. HHS | NIH | National Institute of General Medical Sciences 10.13039/100000057 National Institute of General Medical Sciences

    Region: Americas

    gov (National government)

    Labels2
    1. U.S. National Institute of General Medical Sciences
    2. NIGMS
    Awards1
    1. GM43601

@article{Chen_2016, title={Structural basis for dynamic regulation of the human 26S proteasome}, volume={113}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.1614614113}, DOI={10.1073/pnas.1614614113}, number={46}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Chen, Shuobing and Wu, Jiayi and Lu, Ying and Ma, Yong-Bei and Lee, Byung-Hoon and Yu, Zhou and Ouyang, Qi and Finley, Daniel J. and Kirschner, Marc W. and Mao, Youdong}, year={2016}, month=oct, pages={12991–12996} }