+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21107 | ||||||||||||
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Title | RSC core | ||||||||||||
Map data | RSC core structure | ||||||||||||
Sample |
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Keywords | Chromatin remodeler / RSC / GENE REGULATION | ||||||||||||
Function / homology | Function and homology information regulation of sporulation resulting in formation of a cellular spore / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / plasmid maintenance / DNA translocase activity / RSC-type complex / UV-damage excision repair / sister chromatid cohesion / SWI/SNF complex / nucleosome disassembly ...regulation of sporulation resulting in formation of a cellular spore / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / plasmid maintenance / DNA translocase activity / RSC-type complex / UV-damage excision repair / sister chromatid cohesion / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / nuclear chromosome / sporulation resulting in formation of a cellular spore / rRNA transcription / chromosome, centromeric region / nucleosome binding / ATP-dependent activity, acting on DNA / meiotic cell cycle / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / cytoskeleton organization / lysine-acetylated histone binding / helicase activity / chromosome segregation / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / base-excision repair / chromatin DNA binding / G2/M transition of mitotic cell cycle / double-strand break repair via nonhomologous end joining / double-strand break repair / histone binding / DNA helicase / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / structural molecule activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.07 Å | ||||||||||||
Authors | Patel AB / Moore CM | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Elife / Year: 2019 Title: Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement. Authors: Avinash B Patel / Camille M Moore / Basil J Greber / Jie Luo / Stefan A Zukin / Jeff Ranish / Eva Nogales / Abstract: Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The RSC (emodeling the tructure of hromatin) complex, a ...Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The RSC (emodeling the tructure of hromatin) complex, a member of the SWI/SNF chromatin remodeler family, plays critical roles in genome maintenance, transcription, and DNA repair. Here, we report cryo-electron microscopy (cryo-EM) and crosslinking mass spectrometry (CLMS) studies of yeast RSC complex and show that RSC is composed of a rigid tripartite core and two flexible lobes. The core structure is scaffolded by an asymmetric Rsc8 dimer and built with the evolutionarily conserved subunits Sfh1, Rsc6, Rsc9 and Sth1. The flexible ATPase lobe, composed of helicase subunit Sth1, Arp7, Arp9 and Rtt102, is anchored to this core by the N-terminus of Sth1. Our cryo-EM analysis of RSC bound to a nucleosome core particle shows that in addition to the expected nucleosome-Sth1 interactions, RSC engages histones and nucleosomal DNA through one arm of the core structure, composed of the Rsc8 SWIRM domains, Sfh1 and Npl6. Our findings provide structural insights into the conserved assembly process for all members of the SWI/SNF family of remodelers, and illustrate how RSC selects, engages, and remodels nucleosomes. | ||||||||||||
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
Map data | emd_21107.map.gz | 85.4 MB | EMDB map data format | |
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Header (meta data) | emd-21107-v30.xml emd-21107.xml | 40 KB 40 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21107_fsc.xml | 10.2 KB | Display | FSC data file |
Images | emd_21107.png | 45.3 KB | ||
Masks | emd_21107_msk_1.map | 91.1 MB | Mask map | |
Filedesc metadata | emd-21107.cif.gz | 11 KB | ||
Others | emd_21107_half_map_1.map.gz emd_21107_half_map_2.map.gz | 71.2 MB 71.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21107 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21107 | HTTPS FTP |
-Validation report
Summary document | emd_21107_validation.pdf.gz | 912.8 KB | Display | EMDB validaton report |
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Full document | emd_21107_full_validation.pdf.gz | 912.3 KB | Display | |
Data in XML | emd_21107_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | emd_21107_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21107 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21107 | HTTPS FTP |
-Related structure data
Related structure data | 6v8oMC 6v92C C: citing same article (ref.) M: atomic model generated by this map |
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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_21107.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RSC core structure | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.439 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_21107_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: RSC core structure
File | emd_21107_half_map_1.map | ||||||||||||
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Annotation | RSC core structure | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RSC core structure
File | emd_21107_half_map_2.map | ||||||||||||
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Annotation | RSC core structure | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Remodeling the Structure of Chromatin (RSC)
+Supramolecule #1: Remodeling the Structure of Chromatin (RSC)
+Macromolecule #1: High temperature lethal protein 1
+Macromolecule #2: Chromatin structure-remodeling complex protein RSC14
+Macromolecule #3: Chromatin structure-remodeling complex subunit RSC7
+Macromolecule #4: Chromatin structure-remodeling complex subunit RSC2
+Macromolecule #5: Chromatin structure-remodeling complex protein RSC3
+Macromolecule #6: Chromatin structure-remodeling complex subunit RSC4
+Macromolecule #7: Chromatin structure-remodeling complex protein RSC8
+Macromolecule #8: Chromatin structure-remodeling complex protein RSC6
+Macromolecule #9: Chromatin structure-remodeling complex subunit RSC9
+Macromolecule #10: Chromatin structure-remodeling complex protein RSC58
+Macromolecule #11: Chromatin structure-remodeling complex subunit SFH1
+Macromolecule #12: Nuclear protein STH1/NPS1
+Macromolecule #13: Chromatin structure-remodeling complex protein RSC30
+Macromolecule #14: Unknown protein
+Macromolecule #15: Unknown Protein
+Macromolecule #16: Unknown protein
+Macromolecule #17: Unknown Protein
+Macromolecule #18: Unknown Protein
+Macromolecule #19: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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 |