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Yorodumi- PDB-6tda: Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome -
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-Basic information
Entry | Database: PDB / ID: 6tda | ||||||||||||
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Title | Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Chromatin remodeler DNA binding Nucleosome binding ATPase Transcription | ||||||||||||
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 / 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 / base-excision repair / chromatin DNA binding / G2/M transition of mitotic cell cycle / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / double-strand break repair / nucleosome assembly / chromatin organization / histone binding / DNA helicase / chromatin remodeling / protein heterodimerization activity / 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 / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Xenopus laevis (African clawed frog) Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae S288C (yeast) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15 Å | ||||||||||||
Authors | Wagner, F.R. / Dienemann, C. / Wang, H. / Stuetzer, A. / Tegunov, D. / Urlaub, H. / Cramer, P. | ||||||||||||
Funding support | 3items
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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 |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6tda.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6tda.ent.gz | 798 KB | Display | PDB format |
PDBx/mmJSON format | 6tda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tda_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6tda_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6tda_validation.xml.gz | 113.8 KB | Display | |
Data in CIF | 6tda_validation.cif.gz | 187.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/6tda ftp://data.pdbj.org/pub/pdb/validation_reports/td/6tda | HTTPS FTP |
-Related structure data
Related structure data | 10465MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 10 types, 14 molecules AEBFCGDHQSTUVX
#1: Protein | Mass: 15303.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS #4: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 #13: Protein | | Mass: 9192.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q9URQ5 #15: Protein | | Mass: 156982.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P32597, DNA helicase #16: Protein | | Mass: 54613.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q12406 #17: Protein | | Mass: 53366.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q05123 #18: Protein | | Mass: 18005.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P53330 #19: Protein | | Mass: 32613.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 72876.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 73478.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Chromatin structure-remodeling complex subunit ... , 4 types, 4 molecules KMNR
#7: Protein | Mass: 48833.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q06168 |
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#9: Protein | Mass: 49716.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P32832 |
#10: Protein | Mass: 65289.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q03124 |
#14: Protein | Mass: 72372.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q02206 |
-Chromatin structure-remodeling complex protein ... , 3 types, 3 molecules LOP
#8: Protein | Mass: 126489.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P43609 |
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#11: Protein | Mass: 54222.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P25632 |
#12: Protein | Mass: 57871.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q07979 |
-Non-polymers , 1 types, 1 molecules
#20: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.6 | |||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 45.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 15 Å / Resolution method: OTHER / Num. of particles: 372442 / Symmetry type: POINT |