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- PDB-6v8o: RSC core -

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Entry
Database: PDB / ID: 6v8o
TitleRSC core
Components
  • (Chromatin structure-remodeling complex protein ...) x 6
  • (Chromatin structure-remodeling complex subunit ...) x 5
  • (Unknown Protein) x 3
  • (Unknown protein) x 2
  • High temperature lethal protein 1
  • Nuclear protein STH1/NPS1
KeywordsGENE REGULATION / Chromatin remodeler / RSC
Function / homology
Function and homology information


regulation of sporulation resulting in formation of a cellular spore / regulation of nuclear cell cycle DNA replication / chromatin remodeling at centromere / plasmid maintenance / transfer RNA gene-mediated silencing / RSC-type complex / DNA translocase activity / nucleosome disassembly / UV-damage excision repair / nucleosome positioning ...regulation of sporulation resulting in formation of a cellular spore / regulation of nuclear cell cycle DNA replication / chromatin remodeling at centromere / plasmid maintenance / transfer RNA gene-mediated silencing / RSC-type complex / DNA translocase activity / nucleosome disassembly / UV-damage excision repair / nucleosome positioning / SWI/SNF complex / sister chromatid cohesion / ATP-dependent chromatin remodeling / rRNA transcription / sporulation resulting in formation of a cellular spore / chromosome, centromeric region / DNA-dependent ATPase activity / transcription elongation from RNA polymerase II promoter / cytoskeleton organization / meiotic cell cycle / positive regulation of transcription elongation from RNA polymerase II promoter / chromosome segregation / lysine-acetylated histone binding / base-excision repair / double-strand break repair via homologous recombination / double-strand break repair / transcription coregulator activity / rRNA processing / cellular response to hydrogen peroxide / helicase activity / DNA helicase / DNA helicase activity / double-strand break repair via nonhomologous end joining / G2/M transition of mitotic cell cycle / histone binding / chromatin remodeling / sequence-specific DNA binding / transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / ATPase activity / chromatin binding / regulation of transcription by RNA polymerase II / regulation of transcription, DNA-templated / positive regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus
Snf2-ATP coupling, chromatin remodelling complex / Helicase superfamily 1/2, ATP-binding domain / SMARCC, C-terminal / Snf2, ATP coupling domain / P-loop containing nucleoside triphosphate hydrolase / Chromatin structure-remodeling complex subunit RSC1/RSC2/RSC4 / Bromodomain, conserved site / SANT domain / Chromatin-remodeling complex component Sfh1/SNF5 / Helicase/SANT-associated domain ...Snf2-ATP coupling, chromatin remodelling complex / Helicase superfamily 1/2, ATP-binding domain / SMARCC, C-terminal / Snf2, ATP coupling domain / P-loop containing nucleoside triphosphate hydrolase / Chromatin structure-remodeling complex subunit RSC1/RSC2/RSC4 / Bromodomain, conserved site / SANT domain / Chromatin-remodeling complex component Sfh1/SNF5 / Helicase/SANT-associated domain / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Winged helix-like DNA-binding domain superfamily / Chromatin structure-remodeling complex protein Rsc14 / Homeobox-like domain superfamily / SWIRM domain / SNF5/SMARCB1/INI1 / DNA-binding RFX-type winged-helix domain / Helicase, C-terminal / Zn(2)-C6 fungal-type DNA-binding domain / Bromo adjacent homology (BAH) domain / SANT/Myb domain / Rsc1/Rsc2, bromodomain / Bromodomain-like superfamily / SNF2-related domain / Fungal Zn(2)-Cys(6) binuclear cluster domain / HSA / Helicase conserved C-terminal domain / SNF2 family N-terminal domain / SNF5 / SMARCB1 / INI1 / SWIRM-associated region 1 / SWIRM domain / Zinc finger, ZZ type / Myb-like DNA-binding domain / BAH domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Bromodomain / Chromatin remodelling complex Rsc7/Swp82 subunit / RSC complex, Rsc14/Ldb7 subunit / Bromo adjacent homology (BAH) domain superfamily / Zinc finger, ZZ-type superfamily / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / SNF2-like, N-terminal domain superfamily / Remodelling complex subunit Rsc/polybromo / SWIB/MDM2 domain superfamily / Zinc finger, ZZ-type / Bromodomain
Chromatin structure-remodeling complex subunit SFH1 / Chromatin structure-remodeling complex subunit RSC7 / Chromatin structure-remodeling complex protein RSC6 / Nuclear protein STH1/NPS1 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex protein RSC14 / Chromatin structure-remodeling complex subunit RSC2 / Chromatin structure-remodeling complex protein RSC8 / Chromatin structure-remodeling complex subunit RSC4 / High temperature lethal protein 1 ...Chromatin structure-remodeling complex subunit SFH1 / Chromatin structure-remodeling complex subunit RSC7 / Chromatin structure-remodeling complex protein RSC6 / Nuclear protein STH1/NPS1 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex protein RSC14 / Chromatin structure-remodeling complex subunit RSC2 / Chromatin structure-remodeling complex protein RSC8 / Chromatin structure-remodeling complex subunit RSC4 / High temperature lethal protein 1 / Chromatin structure-remodeling complex subunit RSC9 / Chromatin structure-remodeling complex protein RSC3 / Chromatin structure-remodeling complex protein RSC58
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsPatel, A.B. / Moore, C.M. / Greber, B.J. / Nogales, E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM63072 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM127018 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)U24GM129547 United States
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
C: High temperature lethal protein 1
D: Chromatin structure-remodeling complex protein RSC14
E: Chromatin structure-remodeling complex subunit RSC7
F: Chromatin structure-remodeling complex subunit RSC2
G: Chromatin structure-remodeling complex protein RSC3
H: Chromatin structure-remodeling complex subunit RSC4
I: Chromatin structure-remodeling complex protein RSC8
J: Chromatin structure-remodeling complex protein RSC8
K: Chromatin structure-remodeling complex protein RSC8
L: Chromatin structure-remodeling complex protein RSC8
M: Chromatin structure-remodeling complex protein RSC6
N: Chromatin structure-remodeling complex subunit RSC9
O: Chromatin structure-remodeling complex protein RSC58
Q: Chromatin structure-remodeling complex subunit SFH1
R: Nuclear protein STH1/NPS1
S: Chromatin structure-remodeling complex protein RSC30
2: Unknown protein
3: Unknown Protein
4: Unknown Protein
5: Unknown protein
6: Unknown Protein
7: Unknown Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,105,46223
Polymers1,105,39722
Non-polymers651
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules CR

#1: Protein High temperature lethal protein 1 / Chromatin structure-remodeling complex protein HTL1


Mass: 9192.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q9URQ5
#12: Protein Nuclear protein STH1/NPS1 / ATP-dependent helicase STH1 / Chromatin structure-remodeling complex protein STH1 / SNF2 homolog


Mass: 156982.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32597, DNA helicase

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Chromatin structure-remodeling complex protein ... , 6 types, 9 molecules DGIJKLMOS

#2: Protein Chromatin structure-remodeling complex protein RSC14 / Low dye-binding protein 7 / Remodel the structure of chromatin complex subunit 14


Mass: 19825.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38210
#5: Protein Chromatin structure-remodeling complex protein RSC3 / Remodel the structure of chromatin complex subunit 3


Mass: 101819.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06639
#7: Protein
Chromatin structure-remodeling complex protein RSC8 / Remodel the structure of chromatin complex subunit 8 / SWI3 homolog


Mass: 63253.965 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P43609
#8: Protein Chromatin structure-remodeling complex protein RSC6 / Remodel the structure of chromatin complex subunit 6


Mass: 54222.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25632
#10: Protein Chromatin structure-remodeling complex protein RSC58 / Remodel the structure of chromatin complex subunit 58


Mass: 57871.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q07979
#13: Protein Chromatin structure-remodeling complex protein RSC30 / Remodel the structure of chromatin complex subunit 30


Mass: 101448.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38781

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Chromatin structure-remodeling complex subunit ... , 5 types, 5 molecules EFHNQ

#3: Protein Chromatin structure-remodeling complex subunit RSC7 / Nuclear protein localization protein 6 / Remodel the structure of chromatin complex subunit 7


Mass: 49716.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32832
#4: Protein Chromatin structure-remodeling complex subunit RSC2 / RSC complex subunit RSC2 / Remodel the structure of chromatin complex subunit 2


Mass: 102443.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06488
#6: Protein Chromatin structure-remodeling complex subunit RSC4 / RSC complex subunit RSC4 / Remodel the structure of chromatin complex subunit 4


Mass: 72372.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02206
#9: Protein Chromatin structure-remodeling complex subunit RSC9 / RSC complex subunit RSC9 / Remodel the structure of chromatin complex subunit 9


Mass: 65289.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03124
#11: Protein Chromatin structure-remodeling complex subunit SFH1 / RSC complex subunit SFH1 / SNF5 homolog 1


Mass: 48833.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06168

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Protein/peptide , 5 types, 6 molecules 234567

#14: Protein/peptide Unknown protein


Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#15: Protein/peptide Unknown Protein


Mass: 1635.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#16: Protein/peptide Unknown protein


Mass: 1209.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#17: Protein/peptide Unknown Protein


Mass: 1294.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
#18: Protein/peptide Unknown Protein


Mass: 4188.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Non-polymers , 1 types, 1 molecules

#19: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Remodeling the Structure of Chromatin (RSC) / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Molecular weightValue: 1.1 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1920066 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00425543
ELECTRON MICROSCOPYf_angle_d0.50834555
ELECTRON MICROSCOPYf_dihedral_angle_d12.169565
ELECTRON MICROSCOPYf_chiral_restr0.0393971
ELECTRON MICROSCOPYf_plane_restr0.0034440

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