Journal: Nature / Year: 2020 Title: Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome. Authors: Felix R Wagner / Christian Dienemann / Haibo Wang / Alexandra Stützer / Dimitry Tegunov / Henning Urlaub / Patrick Cramer / Abstract: Chromatin-remodelling complexes of the SWI/SNF family function in the formation of nucleosome-depleted, transcriptionally active promoter regions (NDRs). In the yeast Saccharomyces cerevisiae, the ...Chromatin-remodelling complexes of the SWI/SNF family function in the formation of nucleosome-depleted, transcriptionally active promoter regions (NDRs). In the yeast Saccharomyces cerevisiae, the essential SWI/SNF complex RSC contains 16 subunits, including the ATP-dependent DNA translocase Sth1. RSC removes nucleosomes from promoter regions and positions the specialized +1 and -1 nucleosomes that flank NDRs. Here we present the cryo-electron microscopy structure of RSC in complex with a nucleosome substrate. The structure reveals that RSC forms five protein modules and suggests key features of the remodelling mechanism. The body module serves as a scaffold for the four flexible modules that we call DNA-interacting, ATPase, arm and actin-related protein (ARP) modules. The DNA-interacting module binds extra-nucleosomal DNA and is involved in the recognition of promoter DNA elements that influence RSC functionality. The ATPase and arm modules sandwich the nucleosome disc with the Snf2 ATP-coupling (SnAC) domain and the finger helix, respectively. The translocase motor of the ATPase module engages with the edge of the nucleosome at superhelical location +2. The mobile ARP module may modulate translocase-nucleosome interactions to regulate RSC activity. The RSC-nucleosome structure provides a basis for understanding NDR formation and the structure and function of human SWI/SNF complexes that are frequently mutated in cancer.
History
Deposition
Nov 8, 2019
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Header (metadata) release
Dec 25, 2019
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Map release
Mar 18, 2020
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Update
Mar 27, 2024
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Current status
Mar 27, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Entire : Chromatin remodelling complex RSC ('remodels the structure of chr...
Entire
Name: Chromatin remodelling complex RSC ('remodels the structure of chromatin') bound to a nucleosome
Components
Complex: Chromatin remodelling complex RSC ('remodels the structure of chromatin') bound to a nucleosome
Complex: RSC core
Protein or peptide: Chromatin structure-remodeling complex subunit SFH1
Protein or peptide: Chromatin structure-remodeling complex protein RSC8
Protein or peptide: Chromatin structure-remodeling complex subunit RSC7
Protein or peptide: Chromatin structure-remodeling complex subunit RSC9
Protein or peptide: Chromatin structure-remodeling complex protein RSC6
Protein or peptide: Chromatin structure-remodeling complex protein RSC58
Protein or peptide: High temperature lethal protein 1
Protein or peptide: Chromatin structure-remodeling complex subunit RSC4
Protein or peptide: Nuclear protein STH1/NPS1
Protein or peptide: Actin-related protein 7
Protein or peptide: Actin-like protein ARP9
Protein or peptide: Regulator of Ty1 transposition protein 102
Protein or peptide: Unknown protein
Complex: ATPase domain of Sth1 bound to the nucleosome
Protein or peptide: Histone H3.2
Protein or peptide: Histone H4
Protein or peptide: Histone H2A
Protein or peptide: Histone H2B 1.1
Complex: DNA
DNA: DNA-I
DNA: DNA-J
Ligand: ZINC ION
+
Supramolecule #1: Chromatin remodelling complex RSC ('remodels the structure of chr...
Supramolecule
Name: Chromatin remodelling complex RSC ('remodels the structure of chromatin') bound to a nucleosome type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
+
Supramolecule #2: RSC core
Supramolecule
Name: RSC core / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #7-#19 Details: Composite map 8 made by Warp using the maps 4, 5, 6.
Source (natural)
Organism: Saccharomyces cerevisiae S288C (yeast)
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Supramolecule #3: ATPase domain of Sth1 bound to the nucleosome
Supramolecule
Name: ATPase domain of Sth1 bound to the nucleosome / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#4 / Details: Composite map 7 made by Warp using the maps 2, 3.
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