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Yorodumi- EMDB-10465: Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10465 | ||||||||||||
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Title | Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome | ||||||||||||
Map data | verall density of RSC bound to the nucleosome. | ||||||||||||
Sample |
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Keywords | Chromatin remodeler DNA binding Nucleosome binding ATPase Transcription / DNA BINDING PROTEIN | ||||||||||||
Function / homology | Function and homology information RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / Platelet degranulation / DNA translocase activity / RSC-type complex / SWI/SNF complex / nucleosome disassembly ...RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / Platelet degranulation / DNA translocase activity / RSC-type complex / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / nuclear chromosome / NuA4 histone acetyltransferase complex / rRNA transcription / chromosome, centromeric region / nucleosome binding / ATP-dependent activity, acting on DNA / cytoskeleton organization / meiotic cell cycle / helicase activity / chromosome segregation / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / base-excision repair / chromatin DNA binding / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / G2/M transition of mitotic cell cycle / nucleosome / double-strand break repair / nucleosome assembly / chromatin organization / histone binding / DNA helicase / chromatin remodeling / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / structural molecule activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.0 Å | ||||||||||||
Authors | Wagner FR / Dienemann C | ||||||||||||
Funding support | 3 items
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Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
-Validation report
Summary document | emd_10465_validation.pdf.gz | 526.7 KB | Display | EMDB validaton report |
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Full document | emd_10465_full_validation.pdf.gz | 526.3 KB | Display | |
Data in XML | emd_10465_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_10465_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10465 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10465 | HTTPS FTP |
-Related structure data
Related structure data | 6tdaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10465.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | verall density of RSC bound to the nucleosome. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Mask #4
+Mask #5
+Mask #6
+Additional map: Half-map 2 corresponding to map 8.
+Additional map: Half-map 2 corresponding to map 5.
+Additional map: Half-map 1 corresponding to map 5.
+Additional map: Map 5. Focused map of the body 1
+Additional map: Half-map 2 corresponding to map 4.
+Additional map: Half-map 1 corresponding to map 4.
+Additional map: Half-map 2 corresponding to map 3.
+Additional map: Half-map 1 corresponding to map 3.
+Additional map: Map 3. Focused map of the ATPase domain
+Additional map: Half-map 2 corresponding to map 2.
+Additional map: Half-map 1 corresponding to map 2.
+Additional map: Half-map 1 corresponding to map 8.
+Additional map: Focused map of the nucleosome.
+Additional map: Map 4. Focused map of the arm module.
+Additional map: Map 8. Composite map of the RSC
+Additional map: Half-map 2 corresponding to map 7.
+Additional map: Half-map 1 corresponding to map 7.
+Additional map: Map7. Composite map of the ATPase
+Additional map: Half-map 2 corresponding to map 6.
+Additional map: Half-map 1 corresponding to map 6.
+Additional map: Map 6. Focused map of the body 2
-Sample components
+Entire : Chromatin remodelling complex RSC ('remodels the structure of chr...
+Supramolecule #1: Chromatin remodelling complex RSC ('remodels the structure of chr...
+Supramolecule #2: RSC core
+Supramolecule #3: ATPase domain of Sth1 bound to the nucleosome
+Supramolecule #4: DNA
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: Chromatin structure-remodeling complex subunit SFH1
+Macromolecule #8: Chromatin structure-remodeling complex protein RSC8
+Macromolecule #9: Chromatin structure-remodeling complex subunit RSC7
+Macromolecule #10: Chromatin structure-remodeling complex subunit RSC9
+Macromolecule #11: Chromatin structure-remodeling complex protein RSC6
+Macromolecule #12: Chromatin structure-remodeling complex protein RSC58
+Macromolecule #13: High temperature lethal protein 1
+Macromolecule #14: Chromatin structure-remodeling complex subunit RSC4
+Macromolecule #15: Nuclear protein STH1/NPS1
+Macromolecule #16: Actin-related protein 7
+Macromolecule #17: Actin-like protein ARP9
+Macromolecule #18: Regulator of Ty1 transposition protein 102
+Macromolecule #19: Unknown protein
+Macromolecule #5: DNA-I
+Macromolecule #6: DNA-J
+Macromolecule #20: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL / Details: CryoSPARC |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Number images used: 372442 |
Initial angle assignment | Type: COMMON LINE / Details: CryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Details: RELION |