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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21114 | |||||||||
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Title | RSC-NCP locked | |||||||||
![]() | RSC bound to acetylated nucleosome | |||||||||
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![]() | Chromatin remodeler / RSC / GENE REGULATION / GENE REGULATION-DNA complex | |||||||||
Function / homology | ![]() regulation of sporulation resulting in formation of a cellular spore / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / regulation of nuclear cell cycle DNA replication / plasmid maintenance / Platelet degranulation / npBAF complex ...regulation of sporulation resulting in formation of a cellular spore / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / regulation of nuclear cell cycle DNA replication / plasmid maintenance / Platelet degranulation / npBAF complex / brahma complex / nBAF complex / DNA translocase activity / nucleosome disassembly / RSC-type complex / UV-damage excision repair / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / SWI/SNF complex / nuclear chromosome / sporulation resulting in formation of a cellular spore / NuA4 histone acetyltransferase complex / rRNA transcription / chromosome, centromeric region / negative regulation of megakaryocyte differentiation / anatomical structure morphogenesis / ATP-dependent activity, acting on DNA / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / epigenetic regulation of gene expression / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / cytoskeleton organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / helicase activity / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / meiotic cell cycle / PRC2 methylates histones and DNA / innate immune response in mucosa / Defective pyroptosis / chromosome segregation / HDACs deacetylate histones / transcription elongation by RNA polymerase II / RNA Polymerase I Promoter Escape / positive regulation of transcription elongation by RNA polymerase II / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / transcription coregulator activity / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / base-excision repair / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / chromatin DNA binding / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / double-strand break repair via nonhomologous end joining / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / G2/M transition of mitotic cell cycle / UCH proteinases / nucleosome / double-strand break repair / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.0 Å | |||||||||
![]() | Patel AB / Moore CM / Greber BJ / Nogales E | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 44.9 KB 44.9 KB | Display Display | ![]() |
Images | ![]() | 43.4 KB | ||
Filedesc metadata | ![]() | 13.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 378.9 KB | Display | ![]() |
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Full document | ![]() | 378.5 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Data in CIF | ![]() | 6.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v92MC ![]() 6v8oC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | RSC bound to acetylated nucleosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : RSC-NCP complex
+Supramolecule #1: RSC-NCP complex
+Macromolecule #1: Actin-related protein 7
+Macromolecule #2: Nuclear protein STH1/NPS1
+Macromolecule #3: Actin-like protein ARP9
+Macromolecule #4: Regulator of Ty1 transposition protein 102
+Macromolecule #5: High temperature lethal protein 1
+Macromolecule #6: Chromatin structure-remodeling complex protein RSC14
+Macromolecule #7: Chromatin structure-remodeling complex subunit RSC7
+Macromolecule #8: Chromatin structure-remodeling complex subunit RSC2
+Macromolecule #9: Chromatin structure-remodeling complex protein RSC3
+Macromolecule #10: Chromatin structure-remodeling complex subunit RSC4
+Macromolecule #11: Chromatin structure-remodeling complex protein RSC8
+Macromolecule #12: Chromatin structure-remodeling complex protein RSC6
+Macromolecule #13: Chromatin structure-remodeling complex subunit RSC9
+Macromolecule #14: Chromatin structure-remodeling complex protein RSC58
+Macromolecule #15: Chromatin structure-remodeling complex subunit SFH1
+Macromolecule #16: Chromatin structure-remodeling complex protein RSC30
+Macromolecule #17: Unknown Protein
+Macromolecule #18: Unknown Protein
+Macromolecule #19: Unknown Protein
+Macromolecule #20: Uuknown Protein
+Macromolecule #21: Unknown Protein
+Macromolecule #23: Histone H3.1
+Macromolecule #24: Histone H4
+Macromolecule #25: Histone H2A type 1-B/E
+Macromolecule #26: Histone H2B type 1-K
+Macromolecule #22: DNA (146-MER)
+Macromolecule #27: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Grid | Details: unspecifed |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 13337 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |