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:

Structural insights into assembly and function of the RSC chromatin remodeling complex

Nature Structural & Molecular Biology volume 28, pages 71–80 (2021)Cite this article

Subjects

Abstract

SWI/SNF chromatin remodelers modify the position and spacing of nucleosomes and, in humans, are linked to cancer. To provide insights into the assembly and regulation of this protein family, we focused on a subcomplex of the Saccharomyces cerevisiae RSC comprising its ATPase (Sth1), the essential actin-related proteins (ARPs) Arp7 and Arp9 and the ARP-binding protein Rtt102. Cryo-EM and biochemical analyses of this subcomplex shows that ARP binding induces a helical conformation in the helicase-SANT–associated (HSA) domain of Sth1. Surprisingly, the ARP module is rotated 120° relative to the full RSC about a pivot point previously identified as a regulatory hub in Sth1, suggesting that large conformational changes are part of Sth1 regulation and RSC assembly. We also show that a conserved interaction between Sth1 and the nucleosome acidic patch enhances remodeling. As some cancer-associated mutations dysregulate rather than inactivate SWI/SNF remodelers, our insights into RSC complex regulation advance a mechanistic understanding of chromatin remodeling in disease states.

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 Sth1−Arp7−Arp9−Rtt102 RSC subcomplex (RSCSAR) bound to a nucleosome.
Fig. 2: The structure of the HSA–postHSA–P1 regulatory hub changes in the presence of the ARPs.
Fig. 3: Binding of the ARP module induces folding of the HSA helix.
Fig. 4: RSCSAR peels off nucleosomal DNA at the exit site.
Fig. 5: A basic stretch in Sth1 binds to the nucleosome acidic patch.
Fig. 6: Mutations in a basic region of Sth1 disrupt nucleosome remodeling.
Fig. 7: The ARP module: assembly and regulatory role in the RSC complex.

Similar content being viewed by others

Data availability

The cryo-EM maps for apo RSCSAR (Sth1HSA–Arp7–Arp9–Rtt102 model) are deposited in the EMDB as EMD-21489 and molecular models are deposited in the wwPDB as PDB 6VZG. The cryo-EM maps for RSCSAR bound to the nucleosome in the presence of ADP BeF3 are deposited in the EMDB as EMD-21484 and molecular models are deposited in the wwPDB as PDB 6VZ4. The cryo-EM maps of RSCSAR bound to the nucleosome in the presence of ADP-BeF3 with a peeled DNA conformation are deposited in the EMDB as EMD-21493. Unsharpened, sharpened and half maps were deposited for each EMDB entry.

References

  1. Bartholomew, B. Regulating the chromatin landscape: structural and mechanistic perspectives. Annu. Rev. Biochem. 83, 671–696 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Clapier, C. R. & Cairns, B. R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273–304 (2009).

    Article  CAS  PubMed  Google Scholar 

  3. Kwon, H., Imbalzano, A. N., Khavari, P. A., Kingston, R. E. & Green, M. R. Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex. Nature 370, 477–481 (1994).

    Article  CAS  PubMed  Google Scholar 

  4. Parnell, T. J., Huff, J. T. & Cairns, B. R. RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes. EMBO J. 27, 100–110 (2008).

    Article  CAS  PubMed  Google Scholar 

  5. Cairns, B. R., Levinson, R. S., Yamamoto, K. R. & Kornberg, R. D. Essential role of Swp73p in the function of yeast Swi/Snf complex. Genes Dev. 10, 2131–2144 (1996).

    Article  CAS  PubMed  Google Scholar 

  6. Stern, M., Jensen, R. & Herskowitz, I. Five SWI genes are required for expression of the HO gene in yeast. J. Mol. Biol. 178, 853–868 (1984).

    Article  CAS  PubMed  Google Scholar 

  7. Kadoch, C. & Crabtree, G. R. Mammalian SWI/SNF chromatin remodeling complexes and cancer: mechanistic insights gained from human genomics. Sci. Adv. 1, e1500447 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Reisman, D., Glaros, S. & Thompson, E. A. The SWI/SNF complex and cancer. Oncogene 28, 1653–1668 (2009).

    Article  CAS  PubMed  Google Scholar 

  9. Shain, A. H. & Pollack, J. R. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. PLoS ONE 8, e55119 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  10. Kadoch, C. et al. Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. Nat. Genet. 45, 592–601 (2013).

  11. Wang, X. et al. Oncogenesis caused by loss of the SNF5 tumor suppressor is dependent on activity of BRG1, the ATPase of the SWI/SNF chromatin remodeling complex. Cancer Res. 69, 8094 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Peterson, C. L., Zhao, Y. & Chait, B. T. Subunits of the yeast SWI/SNF complex are members of the actin-related protein (ARP) family. J. Biol. Chem. 273, 23641–23644 (1998).

    Article  CAS  PubMed  Google Scholar 

  13. Zhao, K. et al. Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling. Cell 95, 625–636 (1998).

    Article  CAS  PubMed  Google Scholar 

  14. Schubert, H. L. et al. Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler. Proc. Natl Acad. Sci. USA 110, 3345–3350 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Szerlong, H. et al. The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nat. Struct. Mol. Biol. 15, 469–476 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Turegun, B., Baker, R. W., Leschziner, A. E. & Dominguez, R. Actin-related proteins regulate the RSC chromatin remodeler by weakening intramolecular interactions of the Sth1 ATPase. Commun. Biol. 1, 1 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Clapier, C. R. et al. Regulation of DNA translocation efficiency within the chromatin remodeler RSC/Sth1 potentiates nucleosome sliding and ejection. Mol. Cell 62, 453–461 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Liu, X., Li, M., Xia, X., Li, X. & Chen, Z. Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure. Nature 544, 440 (2017).

    Article  CAS  PubMed  Google Scholar 

  19. Patel, A. B. et al. Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement. Elife 8, e54449 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Wagner, F. R. et al. Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome. Nature https://doi.org/10.1038/s41586-020-2088-0 (2020).

  21. Ye, Y. et al. Structure of the RSC complex bound to the nucleosome. Science 366, 838–843 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Han, Y., Reyes, A. A., Malik, S. & He, Y. Cryo-EM structure of SWI/SNF complex bound to a nucleosome. Nature https://doi.org/10.1038/s41586-020-2087-1 (2020).

  23. He, S. et al. Structure of nucleosome-bound human BAF complex. Science 367, 875 (2020).

    Article  CAS  PubMed  Google Scholar 

  24. Eastlund, A., Malik, S. S. & Fischer, C. J. Kinetic mechanism of DNA translocation by the RSC molecular motor. Arch. Biochem. Biophys. 532, 73–83 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Malik, S. S., Rich, E., Viswanathan, R., Cairns, B. R. & Fischer, C. J. Allosteric interactions of DNA and nucleotides with S. cerevisiae RSC. Biochemistry 50, 7881–7890 (2011).

    Article  CAS  PubMed  Google Scholar 

  26. Sirinakis, G. et al. The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. EMBO J. 30, 2364–2372 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Li, M. et al. Mechanism of DNA translocation underlying chromatin remodelling by Snf2. Nature 567, 409–413 (2019).

    Article  CAS  PubMed  Google Scholar 

  28. Xia, X., Liu, X., Li, T., Fang, X. & Chen, Z. Structure of chromatin remodeler Swi2/Snf2 in the resting state. Nat. Struct. Mol. Biol. 23, 722–729 (2016).

    Article  CAS  PubMed  Google Scholar 

  29. Nakane, T., Kimanius, D., Lindahl, E., Scheres, S. H. & Brunger, A. T. Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION. Elife 7, e36861 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  30. Armache, K.-J., Garlick, J. D., Canzio, D., Narlikar, G. J. & Kingston, R. E. Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 Å resolution. Science 334, 977–982 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Barbera, A. J. et al. The nucleosomal surface as a docking station for Kaposi’s sarcoma herpesvirus LANA. Science 311, 856 (2006).

    Article  CAS  PubMed  Google Scholar 

  32. Kato, H. et al. A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C. Science 340, 1110–1113 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Makde, R. D., England, J. R., Yennawar, H. P. & Tan, S. Structure of RCC1 chromatin factor bound to the nucleosome core particle. Nature 467, 562–566 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. McGinty, R. K., Henrici, R. C. & Tan, S. Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. Nature 514, 591–596 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes. Cell 175, 1272–1288.e20 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Dann, G. P. et al. ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference. Nature 548, 607 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Levendosky, R. F. & Bowman, G. D. Asymmetry between the two acidic patches dictates the direction of nucleosome sliding by the ISWI chromatin remodeler. Elife 8, e45472 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  38. Dao, H. T., Dul, B. E., Dann, G. P., Liszczak, G. P. & Muir, T. W. A basic motif anchoring ISWI to nucleosome acidic patch regulates nucleosome spacing. Nat. Chem. Biol. 16, 134–142 (2020).

    Article  CAS  PubMed  Google Scholar 

  39. Valencia, A. M. et al. Recurrent SMARCB1 mutations reveal a nucleosome acidic patch interaction site that potentiates mSWI/SNF complex chromatin remodeling. Cell 179, 1342–1356.e23 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Dyer, P. N. et al. Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol. 375, 23–44 (2003).

    Article  Google Scholar 

  41. Stark, H. In Methods in Enzymology Vol. 481 (Ed. Jensen, G. J.) 109–126 (Elsevier, 2010).

  42. Herzik, J. M. A., Wu, M. & Lander, G. C. Achieving better-than-3-Å resolution by single-particle cryo-EM at 200 keV. Nat. Methods 14, 1075–1078 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Lander, G. C. et al. Appion: an integrated, database-driven pipeline to facilitate EM image processing. J. Struct. Biol. 166, 95–102 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996).

    Article  CAS  PubMed  Google Scholar 

  45. 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 

  46. Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  47. Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife 7, e42166 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  49. 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 

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

    Article  PubMed  CAS  Google Scholar 

  51. Cianfrocco, M. A., Lahiri, I., DiMaio, F. & Leschziner, A. E. cryoem-cloud-tools: a software platform to deploy and manage cryo-EM jobs in the cloud. J. Struct. Biol. 203, 230–235 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  52. Song, Y. et al. High-resolution comparative modeling with RosettaCM. Structure 21, 1735–1742 (2013).

    Article  CAS  PubMed  Google Scholar 

  53. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).

    Article  CAS  PubMed  Google Scholar 

  54. Alford, R. F. et al. The Rosetta all-atom energy function for macromolecular modeling and design. J. Chem. Theory Comput. 13, 3031–3048 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D Struct. Biol. 74, 531–544 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D Struct. Biol. 75, 861–877 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank the UC San Diego Cryo-Electron Microscopy Facility, which was supported in part by NIH grants to T. Baker and a gift from the Agouron Institute to UCSD and the UC San Diego Physics Computing Facility for IT support. R.W.B. is a Damon Runyon fellow supported by the Damon Runyon Cancer Research Foundation (DRG-2285-16). J.M.R. is a Merck fellow of the Damon Runyon Cancer Research Foundation (DRG-2370-19). B.T. is an American Heart Association pre-doctoral fellow (14PRE19970011). This work was funded by National Institutes of Health grants R01 GM092895 (A.E.L.), R01 GM073791 (R.D.) and T32 AR053461 (P.J.C.).

Author information

Author notes

  1. Richard W. Baker

    Present address: Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

  2. Richard W. Baker

    Present address: Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA

  3. Bengi Turegun

    Present address: Foghorn Therapeutics, Cambridge, MA, USA

  4. These authors contributed equally: Richard W. Baker, Janice M. Reimer.

Authors and Affiliations

  1. Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA

    Richard W. Baker, Janice M. Reimer & Andres E. Leschziner

  2. Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Peter J. Carman, Bengi Turegun & Roberto Dominguez

  3. Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Peter J. Carman

  4. Alliance Protein Laboratories, a Division of KBI BioPharma, San Diego, CA, USA

    Tsutomu Arakawa

  5. Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA

    Andres E. Leschziner

Authors
  1. Richard W. Baker
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Janice M. Reimer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Peter J. Carman
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Bengi Turegun
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tsutomu Arakawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Roberto Dominguez
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Andres E. Leschziner
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

R.W.B., J.M.R., P.J.C. and B.T. performed all of the protein production and purification. R.W.B. performed cryo-EM data collection, analysis and model building. J.M.R. performed nucleosome remodeling assays. T.A. performed CD experiments and analyzed CD data. A.E.L. and R.D. supervised the structural and biochemical work. All authors participated in writing and editing the manuscript.

Corresponding author

Correspondence to Andres E. Leschziner.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Peer reviewer reports are available. Inês Chen and Anke Sparmann were the primary editors on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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

Extended data

Extended Data Fig. 1 Cryo-EM structure determination of the Sth1-Arp7-Arp9-Rtt102 RSC subcomplex (RSCSAR).

a, Workflow for cryo-EM data acquisition and structure determination. Our processing only revealed density for the ARP module. b, Schematic for model building using Coot and Rosetta. Chains from PDB 5TGC and PDB 4I6M were used as a starting model. c, The top 10 Rosetta models were deposited as PDB 6VZG and the top model is shown with its ribbon thickness and color indicating the RMSD among all 10 models. d, The ARP module form SWI/SNF (left) has a single, unbroken α-helix for the HSA domain while that of RSC (right) comprises two α-helices separated by a loop. e, Our cryo-EM has density for a known ATP binding site in Arp7. This site is catalytically dead and the ATP is likely from endogenous ATP pools.

Extended Data Fig. 2 Cryo-EM structure determination of RSCSAR bound to the nucleosome.

a, Workflow for cryo-EM data acquisition and structure determination. b, 3D classification with alignment was used to find ~300,000 particles with better ARP module density. This dataset reached a final global FSC resolution of ~3.9 Å with a local resolution range of 3.4-15 Å. c, Partial signal subtraction followed by 3D classification without alignment was used to identify a sub-set of particles with an alternate DNA conformation at the nucleosome DNA exit site.

Extended Data Fig. 3 Multi-body refinement of RSCSAR bound to the nucleosome in the ADP-BeF3 state.

a, The consensus refinement of RSCSAR-nucleosome from Extended Data Fig. 2b was used to generate 3 masks and as a starting model for multi-body refinement. b, PCA was performed in Relion-3 and used to generate maps that show the conformational heterogeneity present in our data set. Several of these maps are shown overlaid. c, Eigenvalue plots for the top three eigenvectors. d, The maps generated in panel (b) were used to build PDB models. 10 models for each eigenvector were generated and are shown superimposed. The main sources of heterogeneity in our data set are a rocking of the ATPase domain (eigenvector 1) and rocking of the ARP module along two different axes (eigenvector 2 and 3).

Extended Data Fig. 4 Model building of RSCSAR-nucleosome (ADP-BeF3) and comparison with Snf2-nucleosome (ADP-BeF3).

a, Model building schematic for RSCSAR-nucleosome (ADP-BeF3). Snf2-nucleosome (PDB 5Z3U) and the T. thermophilus Snf2 crystal structure (PDB 5HZR) were used as a starting point for model building and refinement using Coot, Rosetta, and phenix.real_space_refine. The ARP module built in Extended Data Fig. 1 was rigid-body docked into the map, yielding a near-complete model for all components in our sample. b, PDB 5Z3U is shown docked into our cryo-EM map. c, The same view as in panel (b) but showing Sth1-nucleosome (ADP-BeF3). d, The top Rosetta model is shown with its ribbon thickness and color indicating the RMSD among the top 10 models. e, The RSCSAR-nucleosome structure is shown with the HSA and postHSA domains of Sth1 colored in a rainbow from N to C terminus. Residues 385-391 are shown as a cylinder to signal the linkage between the two domains and indicate that the density is compatible with an alpha helix, although this region is not included in the deposited.

Extended Data Fig. 5 The ARP module of RSC only interacts with the HSA domain of Sth1.

a, Our model of RSCSAR-nucleosome (ADP-BeF3). b, Model of RSC-nucleosome (PDB 6KW3) shown in the same orientation as panel (a) (left) and rotated 90° (right). The ARP module only interacts with the HSA domain in both RSC and RSCSAR. c, Multiple RSC-nucleosome (ADP-BeF3) cryo-EM structures were aligned. Left, all components shown and colored using the same convention. Right, Arp7–Arp9–Rtt102 and all components of the SRC are omitted to highlight the conformational flexibility of the Sth1 HSA domain (orange) among the three structures. The HSA domain from RSCSAR is included in this panel to indicate that, despite their conformational flexibility, the HSA domains from the three RSC-nucleosome structures have a similar general orientation relative to the HSA from RSCSAR.

Extended Data Fig. 6 Comparison of the nucleosome-bound ATPase domain of Snf2, RSC, and RSCSAR in the ADP-BeF3 nucleotide state.

a, The PDB models for Snf2, RSCSAR, and RSC are shown with the same orientation and domain coloring. All three structures are from S.cerevisae, bound to the nucleosome and in the ADP-BeF3 nucleotide state. b-d, The ATPase domain of each structure from (a) was docked into the cryo-EM map of RSCSAR. The postHSA domain (b), Protrusion 1 domain (c), and Brace Helices (d) were colored according to their respective PDB model in each panel. Cyan: RSCSAR, magenta: RSC (PDB 6KW3), orange: Snf2 (PDB 5Z3U).

Extended Data Fig. 7 Comparison of cryo-EM maps of Snf2-nucleosome in the apo, ADP, and ADP-BeF3 states and RSCSAR-nucleosome (ADP-BeF3).

Each structure is shown with cryo-EM map and corresponding PDB model. All structures are bound to the nucleosome but this region is omitted for clarity. The same map at the same contour level is shown opaque (top) and transparent (bottom). Note that density for the Brace Helix I is absent in the ADP-BeF3 state but present in the apo and ADP-bound states.

Extended Data Fig. 8 Structural comparison of the ATPase domain of SWI/SNF remodelers in the apo, ADP, and ADP-BeF3 nucleotide states.

a, Domain schematic of Sth1 from RSCSAR. b, Structural alignment of the ATPase domain of Snf2 apo with Snf2-ADP (left), Snf2-ADP-BeF3 (middle), and RSCSAR- BeF3 (right). All structures are colored using the domain convention shown in (a). c, All structures from (b) are aligned and colored grey, except for the Brace Helices which are colored by model: Snf2 apo, pink; Snf2 ADP, purple; Snf2 ADP-BeF3, tan; RSCSAR ADP-BeF3, yellow. PDB codes for structures shown: Snf2 apo (5X0Y), ADP (5Z3O), ADP-BeF3 (5Z3U).

Extended Data Fig. 9 Conformation of the nucleosomal DNA in the cryo-EM structure of RSCSAR-nucleosome (ADP-BeF3).

a, The models of Snf2 (PDB 5Z3U) and RSCSAR were aligned. A ribbon representation of the nucleosomal DNA is shown for Snf2 (grey) and Sth1 (colored by SHL). Super Helical Locations for the aligned models are shown inside the cryo-EM density of RSCSAR. b, RSCSAR with a canonical conformation of the nucleosome. Top panel shows map and model from the initial 3.9 Å consensus refinement (Extended Data Fig. 2b). The nucleosomal DNA is colored purple and basic residues in the N-lobe are colored blue. c, RSCSAR with a peeled conformation of the nucleosomal DNA exit site. Top panel shows map and model from the 4.3 Å refinement of a subset of particles with a peeled DNA conformation (Extended Data. Fig. 2c). The nucleosomal DNA is colored orange and basic residues in the N-lobe are colored blue. d, Alignment of canonical and peeled DNA structures. Note that basic residues in the N-lobe appear to make contact with the exit site DNA in the peeled conformation. e, SHL6 shifts between the canonical and peeled DNA conformations.

Extended Data Fig. 10 A basic patch in RSCSAR binds to the nucleosome and is important for remodeling.

a, Different maps from the RSCSAR consensus refinement are shown in the same orientation. A region of unassigned density is circled in yellow b, The same maps shown in panel (a) with red indicating regions of the maps that are not accounted for by the PDB model of the nucleosome. c, Schematic of the RSCSAR construct used in nucleosome remodeling assays. Sequences of Sth1 mutants used for remodeling assays are shown below the wild type sequence. Residues mutated in the RSCSAR-L and RSCSAR-R variants are noted (salmon, L; green, R). d, Remodeling assay of wildtype, RSCSAR-All Alanine, RSCSAR-L, and RSCSAR-R mutants. WT data are the same as in Fig. 6b. e, Remodeling assay of wildtype and RSCSAR-R mutant. f, Remodeling assay of wildtype and RSCSAR-L mutant. Error is reported as standard deviation where n=3 replicates.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Baker, R.W., Reimer, J.M., Carman, P.J. et al. Structural insights into assembly and function of the RSC chromatin remodeling complex. Nat Struct Mol Biol 28, 71–80 (2021). https://doi.org/10.1038/s41594-020-00528-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41594-020-00528-8

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