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Open data
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Basic information
Entry | Database: PDB / ID: 6v8o | ||||||||||||
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Title | RSC core | ||||||||||||
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![]() | GENE REGULATION / Chromatin remodeler / RSC | ||||||||||||
Function / homology | ![]() regulation of sporulation resulting in formation of a cellular spore / 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 / npBAF complex / brahma complex / nBAF complex / DNA translocase activity / nucleosome disassembly ...regulation of sporulation resulting in formation of a cellular spore / 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 / 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 / rRNA transcription / chromosome, centromeric region / ATP-dependent activity, acting on DNA / nucleosomal DNA binding / cytoskeleton organization / helicase activity / meiotic cell cycle / chromosome segregation / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / double-strand break repair via homologous recombination / lysine-acetylated histone binding / base-excision repair / chromatin DNA binding / double-strand break repair via nonhomologous end joining / G2/M transition of mitotic cell cycle / double-strand break repair / histone binding / DNA helicase / sequence-specific DNA binding / transcription coactivator activity / 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 DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å | ||||||||||||
![]() | Patel, A.B. / Moore, C.M. / Greber, B.J. / Nogales, E. | ||||||||||||
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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
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 680.4 KB | Display | ![]() |
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PDB format | ![]() | 483.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 90.4 KB | Display | |
Data in CIF | ![]() | 138.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 21107MC ![]() 6v92C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 2 molecules CR
#1: Protein | Mass: 9192.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q9URQ5 |
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#12: Protein | Mass: 156982.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32597, DNA helicase |
-Chromatin structure-remodeling complex protein ... , 6 types, 9 molecules DGIJKLMOS
#2: Protein | Mass: 19825.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38210 | ||||||
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#5: Protein | Mass: 101819.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06639 | ||||||
#7: Protein | Mass: 63253.965 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P43609 #8: Protein | | Mass: 54222.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P25632 #10: Protein | | Mass: 57871.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q07979 #13: Protein | | Mass: 101448.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38781 |
-Chromatin structure-remodeling complex subunit ... , 5 types, 5 molecules EFHNQ
#3: Protein | Mass: 49716.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32832 |
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#4: Protein | Mass: 102443.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06488 |
#6: Protein | Mass: 72372.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q02206 |
#9: Protein | Mass: 65289.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q03124 |
#11: Protein | Mass: 48833.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q06168 |
-Protein/peptide , 5 types, 6 molecules 234567
#14: Protein/peptide | Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c | ||||||
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#15: Protein/peptide | Mass: 1635.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c #16: Protein/peptide | | Mass: 1209.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c #17: Protein/peptide | | Mass: 1294.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c #18: Protein/peptide | | Mass: 4188.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/ZN.gif)
#19: 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 |
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Sample preparation
Component | Name: Remodeling the Structure of Chromatin (RSC) / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Molecular weight | Value: 1.1 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1920066 / Symmetry type: POINT | ||||||||||||||||||||||||
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