Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Structure of a SIN3–HDAC complex from budding yeast

Nature Structural & Molecular Biology volume 30, pages 753–760 (2023)Cite this article

Subjects

Abstract

SIN3–HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM structure of the budding yeast SIN3–HDAC complex Rpd3L at an average resolution of 2.6 Å. The structure reveals that two distinct arms (ARM1 and ARM2) hang on a T-shaped scaffold formed by two coiled-coil domains. In each arm, Sin3 interacts with different subunits to create a different environment for the histone deacetylase Rpd3. ARM1 is in the inhibited state with the active site of Rpd3 blocked, whereas ARM2 is in an open conformation with the active site of Rpd3 exposed to the exterior space. The observed asymmetric architecture of Rpd3L is different from those of available structures of other class I HDAC complexes. Our study reveals the organization mechanism of the SIN3–HDAC complex and provides insights into the interaction pattern by which it targets histone deacetylase to chromatin.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Cryo-EM structure of the S. cerevisiae Rpd3L complex.
Fig. 2: The scaffold of the Rpd3L complex.
Fig. 3: Sin3 as the organizer of each arm.
Fig. 4: Rpd3 is stabilized by three anchors of Sin3_HID domain.
Fig. 5: Rpd3 in ARM1 is blocked by loop 1 of Rxt2.
Fig. 6: Structure comparison between the Rpd3L complex and other class I HDAC complexes.
Fig. 7: A working model of chromatin recognition and binding for the Rpd3L complex.

Similar content being viewed by others

Data availability

The atomic coordinates have been deposited in the Protein Data Bank with the accession code 8HPO, and the EM maps have been deposited in EMDB with the accession codes EMD-34935, EMD-34936, EMD-34937, EMD-34938 and EMD-34939. Source data are provided with this paper.

References

  1. Vidal, M. & Gaber, R. F. RPD3 encodes a second factor required to achieve maximum positive and negative transcriptional states in Saccharomyces cerevisiae. Mol. Cell. Biol. 11, 6317–6327 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Taunton, J., Hassig, C. A. & Schreiber, S. L. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272, 408–411 (1996).

    Article  CAS  PubMed  Google Scholar 

  3. Verdin, E. & Ott, M. 50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond. Nat. Rev. Mol. Cell Biol. 16, 258–264 (2015).

    Article  CAS  PubMed  Google Scholar 

  4. Micelli, C. & Rastelli, G. Histone deacetylases: structural determinants of inhibitor selectivity. Drug Discov. Today 20, 718–735 (2015).

    Article  CAS  PubMed  Google Scholar 

  5. Yang, X. J. & Seto, E. The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat. Rev. Mol. Cell Biol. 9, 206–218 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Moser, M. A., Hagelkruys, A. & Seiser, C. Transcription and beyond: the role of mammalian class I lysine deacetylases. Chromosoma 123, 67–78 (2014).

    Article  CAS  PubMed  Google Scholar 

  7. Millard, C. J., Watson, P. J., Fairall, L. & Schwabe, J. W. R. Targeting class I histone deacetylases in a “complex” environment. Trends Pharmacol. Sci. 38, 363–377 (2017).

    Article  CAS  PubMed  Google Scholar 

  8. Wang, Z. A. et al. Diverse nucleosome site-selectivity among histone deacetylase complexes. eLife 9, e57663 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Laugesen, A. & Helin, K. Chromatin repressive complexes in stem cells, development, and cancer. Cell Stem Cell 14, 735–751 (2014).

    Article  CAS  PubMed  Google Scholar 

  10. Adams, G. E., Chandru, A. & Cowley, S. M. Co-repressor, co-activator and general transcription factor: the many faces of the Sin3 histone deacetylase (HDAC) complex. Biochem. J. 475, 3921–3932 (2018).

    Article  CAS  PubMed  Google Scholar 

  11. Nascimento, E. M. et al. The opposing transcriptional functions of Sin3a and c-Myc are required to maintain tissue homeostasis. Nat. Cell Biol. 13, 1395–1405 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Kandoth, C. et al. Mutational landscape and significance across 12 major cancer types. Nature 502, 333–339 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kwon, Y. J. et al. Selective inhibition of SIN3 corepressor with avermectins as a novel therapeutic strategy in triple-negative breast cancer. Mol. Cancer Ther. 14, 1824–1836 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Rielland, M. et al. Senescence-associated SIN3B promotes inflammation and pancreatic cancer progression. J. Clin. Invest. 124, 2125–2135 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Falkenberg, K. J. & Johnstone, R. W. Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders. Nat. Rev. Drug Discov. 13, 673–691 (2014).

    Article  CAS  PubMed  Google Scholar 

  16. Adams, M. K. et al. Differential complex formation via paralogs in the human Sin3 protein interaction network. Mol. Cell Proteomics 19, 1468–1484 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Witteveen, J. S. et al. Haploinsufficiency of MeCP2-interacting transcriptional co-repressor SIN3A causes mild intellectual disability by affecting the development of cortical integrity. Nat. Genet. 48, 877–887 (2016).

    Article  CAS  PubMed  Google Scholar 

  18. Latypova, X. et al. Haploinsufficiency of the Sin3/HDAC corepressor complex member SIN3B causes a syndromic intellectual disability/autism spectrum disorder. Am. J. Hum. Genet 108, 929–941 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kasten, M. M., Dorland, S. & Stillman, D. J. A large protein complex containing the yeast Sin3p and Rpd3p transcriptional regulators. Mol. Cell. Biol. 17, 4852–4858 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Keogh, M. C. et al. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123, 593–605 (2005).

    Article  CAS  PubMed  Google Scholar 

  21. Carrozza, M. J. et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123, 581–592 (2005).

    Article  CAS  PubMed  Google Scholar 

  22. van Oevelen, C. et al. A role for mammalian Sin3 in permanent gene silencing. Mol. Cell 32, 359–370 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  23. Kadosh, D. & Struhl, K. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89, 365–371 (1997).

    Article  CAS  PubMed  Google Scholar 

  24. Bing Li et al. Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin. Science 316, 1050–1054 (2007).

    Article  PubMed  Google Scholar 

  25. Silverstein, R. A. & Ekwall, K. Sin3: a flexible regulator of global gene expression and genome stability. Curr. Genet. 47, 1–17 (2005).

    Article  CAS  PubMed  Google Scholar 

  26. Lechner, T. et al. Sds3 (suppressor of defective silencing 3) is an integral component of the yeast Sin3·Rpd3 histone deacetylase complex and is required for histone deacetylase activity. J. Biol. Chem. 275, 40961–40966 (2000).

    Article  CAS  PubMed  Google Scholar 

  27. Lamping, E., Lückl, J., Paltauf, F., Henry, S. A. & Kohlwein, S. D. Isolation and characterization of a mutant of Saccharomyces cerevisiae with pleiotropic deficiencies in transcriptional activation and repression. Genetics 137, 55–65 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Colina, A. R. & Young, D. Raf60, a novel component of the Rpd3 histone deacetylase complex required for Rpd3 activity in Saccharomyces cerevisiae. J. Biol. Chem. 280, 42552–42556 (2005).

    Article  CAS  PubMed  Google Scholar 

  29. Loewith, R. et al. Pho23 is associated with the Rpd3 histone deacetylase and is required for its normal function in regulation of gene expression and silencing in Saccharomyces cerevisiae. J. Biol. Chem. 276, 24068–24074 (2001).

    Article  CAS  PubMed  Google Scholar 

  30. Xie, T. et al. Structure of the 30-kDa Sin3-associated protein (SAP30) in complex with the mammalian Sin3A corepressor and its role in nucleic acid binding. J. Biol. Chem. 286, 27814–27824 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Clark, M. D. et al. Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex. Proc. Natl Acad. Sci. USA 112, E3669–E3678 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Brubaker, K. et al. Solution structure of the interacting domains of the Mad-Sin3 complex: implications for recruitment of a chromatin-modifying complex. Cell 103, 655–665 (2000).

    Article  CAS  PubMed  Google Scholar 

  33. Nomura, M., Uda-Tochio, H., Murai, K., Mori, N. & Nishimura, Y. The neural repressor NRSF/REST binds the PAH1 domain of the Sin3 corepressor by using its distinct short hydrophobic helix. J. Mol. Biol. 354, 903–915 (2005).

    Article  CAS  PubMed  Google Scholar 

  34. Pena, P. V. et al. Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor. J. Mol. Biol. 380, 303–312 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Narumi-Kishimoto, Y. et al. Novel SIN3A mutation identified in a Japanese patient with Witteveen-Kolk syndrome. Eur. J. Med. Genet. 62, 103547 (2019).

    Article  PubMed  Google Scholar 

  36. Bansal, N., David, G., Farias, E. & Waxman, S. Emerging roles of epigenetic regulator Sin3 in cancer. Adv. Cancer Res. 130, 113–135 (2016).

    Article  CAS  PubMed  Google Scholar 

  37. Watanabe, K. et al. A novel somatic mutation of SIN3A detected in breast cancer by whole-exome sequencing enhances cell proliferation through ERα expression. Sci. Rep. 8, 16000 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  38. Ashkenazy, H. et al. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res. 44, W344–W350 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Landau, M. et al. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res. 33, W299–W302 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Laherty, C. D. et al. Histone deacetylases associated with the mSin3 corepressor mediate Mad transcriptional repression. Cell 89, 349–356 (1997).

    Article  CAS  PubMed  Google Scholar 

  41. Finnin, M. S. et al. Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature 401, 188–193 (1999).

    Article  CAS  PubMed  Google Scholar 

  42. Watson, P. J., Fairall, L., Santos, G. M. & Schwabe, J. W. Structure of HDAC3 bound to co-repressor and inositol tetraphosphate. Nature 481, 335–340 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Millard, C. J., Fairall, L., Ragan, T. J., Savva, C. G. & Schwabe, J. W. R. The topology of chromatin-binding domains in the NuRD deacetylase complex. Nucleic Acids Res. https://doi.org/10.1093/nar/gkaa1121 (2020).

  44. Turnbull, R. E. et al. The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure. Nat. Commun. 11, 3252 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Pratap, J. et al. The histone deacetylase inhibitor, vorinostat, reduces tumor growth at the metastatic bone site and associated osteolysis, but promotes normal bone loss. Mol. Cancer Ther. 9, 3210–3220 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Subramanian, S., Bates, S. E., Wright, J. J., Espinoza-Delgado, I. & Piekarz, R. L. Clinical toxicities of histone deacetylase inhibitors. Pharmaceuticals 3, 2751–2767 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Maxon, M. E. & Herskowitz, I. Ash1p is a site-specific DNA-binding protein that actively represses transcription. Proc. Natl Acad. Sci. USA 98, 1495–1500 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Le Guezennec, X., Vermeulen, M. & Stunnenberg, H. G. Molecular characterization of Sin3 PAH-domain interactor specificity and identification of PAH partners. Nucleic Acids Res. 34, 3929–3937 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  49. Strich, R. et al. UME6 is a key regulator of nitrogen repression and meiotic development. Genes Dev. 8, 796–810 (1994).

    Article  CAS  PubMed  Google Scholar 

  50. Lee, B. B. et al. Rpd3L HDAC links H3K4me3 to transcriptional repression memory. Nucleic Acids Res. 46, 8261–8274 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Zhu, C. et al. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 19, 556–566 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Crisp, R. J., Adkins, E. M., Kimmel, E. & Kaplan, J. Recruitment of Tup1p and Cti6p regulates heme-deficient expression of Aft1p target genes. EMBO J. 25, 512–521 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. DeLano, W. L. The PyMOL Molecular Graphics System. http://www.pymol.org (2002).

  54. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  CAS  PubMed  Google Scholar 

  55. Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).

    Article  CAS  PubMed  Google Scholar 

  56. Gietz, R. D. & Schiestl, R. H. Quick and easy yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2, 35–37 (2007).

    Article  CAS  PubMed  Google Scholar 

  57. Yang, B. et al. Identification of cross-linked peptides from complex samples. Nat. Methods 9, 904–906 (2012).

    Article  CAS  PubMed  Google Scholar 

  58. Lei, J. & Frank, J. Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope. J. Struct. Biol. 150, 69–80 (2005).

    Article  PubMed  Google Scholar 

  59. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Kimanius, D., Forsberg, B. O., Scheres, S. H. & Lindahl, E. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. eLife 5, e18722 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  62. Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    Article  CAS  PubMed  Google Scholar 

  64. Zhan, X., Yan, C., Zhang, X., Lei, J. & Shi, Y. Structure of a human catalytic step I spliceosome. Science 359, 537–545 (2018).

    Article  CAS  PubMed  Google Scholar 

  65. Chen, S. X. et al. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135, 24–35 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).

    Article  CAS  PubMed  Google Scholar 

  67. Swint-Kruse, L. & Brown, C. S. Resmap: automated representation of macromolecular interfaces as two-dimensional networks. Bioinformatics 21, 3327–3328 (2005).

    Article  CAS  PubMed  Google Scholar 

  68. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  PubMed  Google Scholar 

  69. Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).

    Article  CAS  PubMed  Google Scholar 

  71. Amunts, A. et al. Structure of the yeast mitochondrial large ribosomal subunit. Science 343, 1485–1489 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–W383 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank Y. Shi for support and suggestions, and the cryo-EM facility and supercomputer center of Westlake University for providing cryo-EM and computation support, respectively. This work was supported by funds from the National Natural Science Foundation of China (32100978 to C.W.).

Author information

Author notes

  1. These authors contributed equally: Zhouyan Guo, Chen Chu.

Authors and Affiliations

  1. College of Life Sciences, Zhejiang University, Hangzhou, China

    Zhouyan Guo & Chen Chu

  2. Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China

    Zhouyan Guo, Chen Chu, Yichen Lu, Xiaofeng Zhang, Xiechao Zhan & Chengcheng Wang

  3. Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China

    Zhouyan Guo, Chen Chu, Yichen Lu, Xiaofeng Zhang, Xiechao Zhan & Chengcheng Wang

  4. Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China

    Zhouyan Guo, Chen Chu, Yichen Lu, Xiaofeng Zhang, Xiechao Zhan & Chengcheng Wang

  5. Department of Chemistry, School of Science, Westlake University, Hangzhou, China

    Yihang Xiao & Mingxuan Wu

  6. Human Nutrition Program & James Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA

    Shuaixin Gao

  7. Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China

    Catherine C. L. Wong

Authors
  1. Zhouyan Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chen Chu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yichen Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xiaofeng Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yihang Xiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Mingxuan Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Shuaixin Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Catherine C. L. Wong
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Xiechao Zhan
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Chengcheng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

C.W. and Z.G. conceived the project and designed the experiments. C.W., Z.G. and C.C. performed the majority of the experiments. X. Zhang contributed to EM sample preparation. X. Zhan and Y.L. carried out the structure determination. Y.X. and M.W. contributed to the preparation of nucleosomes. S.G. and C.C.L.W. performed MS proteomics experiments. C.W., Z.G. and X. Zhan wrote the manuscript.

Corresponding authors

Correspondence to Xiechao Zhan or Chengcheng Wang.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Structural & Molecular Biology thanks the anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available. Primary Handling Editors: Tiago Faial and Carolina Perdigoto, in collaboration with the Nature Structural & Molecular Biology team.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Purification of the Rpd3L complex from S. cerevisiae.

a and b, Gel filtration analysis of the Rpd3L complex purified by 3xFlag-tag on Sin3 (a) or Rxt1 (b). The peak fractions from gel filtration were visualized on SDS-PAGE by Coomassie blue staining or silver staining. Peak Fractions were collected for cryo-EM sample preparation. However, these cryo-EM sample were in bad behavior. c, The peak fractions from glycerol density gradient centrifugation were visualized on SDS-PAGE by silver staining. Fractions 8–12 were collected for cryo-EM sample preparation. We finally used these samples to collect cryo-EM data. These purification experiments have been repeated at least three times.

Source data

Extended Data Fig. 2 Characterization of the Rpd3L complex.

a, Protein components of the purified Rpd3L complex were confirmed by mass spectrometry analysis. b, The cross-linking mass spectrometry (XL-MS) analysis of the Rpd3L complex The purified complex was crosslinked by BS3. This analysis identified 24 pairs of inter-molecular interaction among the Rpd3L proteins. This data facilitates structural identification of the Rpd3L components in the EM density. c, Schematic representation of the intermolecular cross-links within the Rpd3L complex.

Source data

Extended Data Fig. 3 Micrographs, 2D classes and a flow chart of cryo-EM data (Sin3-Flag) processing for the Rpd3L complex.

a, Representative electron micrograph of the Sin3-Flag sample. The dimeter of the green circle is 25 nm. b, 2D classes of the Sin3-Flag sample. c, All processing steps were carried out in RELION 3.0 and cryoSPARC. Please refer to Methods for details.

Extended Data Fig. 4 Micrographs, 2D classes and a flow chart of cryo-EM data (Rxt1-Flag) processing for the Rpd3L complex.

a, Representative electron micrograph of the Rxt1-Flag sample. The dimeter of the green circle is 25 nm. b, 2D classes of the Rxt1-Flag sample. c, All processing steps were carried out in RELION 3.0 and cryoSPARC. Please refer to Methods for details.

Extended Data Fig. 5 Cryo-EM analysis of the yeast Rpd3L complex.

a, The final reconstruction for the Rpd3L complex displays an average resolution of 2.6 Å on the basis of the Fourier-shell correlation (FSC) value of 0.143. b, Two overall views of the EM density map. The local resolutions are color-coded for different regions of Rpd3L complex. c, Angular distribution of the particles used for the reconstruction. d, The FSC curves for cross-validation between the model and the cryo-EM maps of yeast Rpd3L complex. Shown here are the FSC curves between the final refined atomic model and the reconstruction from all particles (black), between the model refined in the reconstruction from only half of the particles and the reconstruction from that same half (red), and between that same model and the reconstruction from the other half of the particles (green).

Extended Data Fig. 6 The structure of the Ash1 (residue 188–221).

Depending on the XL-MS analysis and the AlphaFold model, we docked the region (residue 188–221) of Ash1 in the low-resolution map to interact with the coiled-coil domains of Sds3 and Dep1.

Extended Data Fig. 7 EM density maps for representative segments of the Rpd3L complex.

Close-up views of fragments of the Rpd3L subunits with cryo-EM densities shown as meshes. The bulk residues are shown as sticks representation. Most of the side chains fit into the cryo-EM map well, indicating the model was built correctly.

Extended Data Fig. 8 Structures of Sds3, Dep1, Rxt2 and Pho23.

a, Cartoon models of Sds3, Dep1, Rxt2 and Pho23. b, A close-up view on the interface between Pho23_α1 and the α10 of Sin3. c, A close-up view on the interface between Rxt2_α7 and the α5 of Sin3’. d, The α9-10 of Sin3_HID or Sin3’_HID interacts with Dep1_α5 or Sds3_α4, respectively, which is similar to the NMR structure of human SIN3A-SDS3 subcomplex (PDB code: 2N2H).

Extended Data Fig. 9 Sequence alignment and structural analysis of class I HDACs.

a, The structures of the Rpd3 and Rpd3’ are almost identical and similar to the structure of human HDAC1. b, The binding sites of the zinc metal in the two copies of Rpd3. c, A close-up view of the zinc binding sites.

Extended Data Fig. 10 Superposition of yeast Rpd3-Sin3HID and human HDAC1-MTA1SANT.

The N-terminus of Sin3_α6 is clashed with InsP6.

Supplementary information

Supplementary Information

Supplementary Figs. 1–9, sequence alignments of Sin3, Rpd3, Sds3, Pho23, Sap30, Ume1, Dep1, Rxt2 and Rxt3, and Table 1, summary of model building for the Rpd3L complex.

Reporting Summary

Peer Review File

Source data

Source Data Fig. 1

Unprocessed gel for Fig. 1a.

Source Data Extended Data Fig. 1

Unprocessed gel for Extended Data Fig. 1a–c.

Source Data Extended Data Fig. 2

Source MS data for Extended Data Fig. 2a (Sin3-Flag sample) and Extended Data Fig. 2a (Rxt1-Flag sample), and source cross-linking MS data for Extended Data Fig. 2b,c.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Guo, Z., Chu, C., Lu, Y. et al. Structure of a SIN3–HDAC complex from budding yeast. Nat Struct Mol Biol 30, 753–760 (2023). https://doi.org/10.1038/s41594-023-00975-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41594-023-00975-z

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing