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- PDB-6v8o: RSC core -

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Basic information

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 / plasmid maintenance / DNA translocase activity / nucleosome array spacer activity / RSC-type complex / ATP-dependent chromatin remodeler activity / UV-damage excision repair / nucleosome disassembly ...regulation of sporulation resulting in formation of a cellular spore / : / regulation of nuclear cell cycle DNA replication / plasmid maintenance / DNA translocase activity / nucleosome array spacer activity / RSC-type complex / ATP-dependent chromatin remodeler activity / UV-damage excision repair / nucleosome disassembly / SWI/SNF complex / sister chromatid cohesion / sporulation resulting in formation of a cellular spore / nuclear chromosome / rRNA transcription / histone H4 reader activity / chromosome, centromeric region / nucleosome binding / : / cytoskeleton organization / meiotic cell cycle / transcription coregulator activity / chromosome segregation / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / helicase activity / double-strand break repair via homologous recombination / 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 / sequence-specific DNA binding / DNA helicase / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive 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
Chromatin structure-remodeling complex protein Rsc14 / RSC complex, Rsc14/Ldb7 subunit / : / Rsc1/Rsc2, bromodomain / : / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / : / RSC4 Ig-like domain / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit ...Chromatin structure-remodeling complex protein Rsc14 / RSC complex, Rsc14/Ldb7 subunit / : / Rsc1/Rsc2, bromodomain / : / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / : / RSC4 Ig-like domain / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / DNA-binding RFX-type winged-helix domain / RFX-type winged-helix DNA-binding domain profile. / : / Chromatin-remodeling complex component Sfh1/SNF5 / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Remodelling complex subunit Rsc/polybromo / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / Bromo adjacent homology domain / SWIB/MDM2 domain superfamily / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / SANT domain profile. / SANT domain / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Myb-like DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chromatin structure-remodeling complex protein RSC6 / Nuclear protein STH1/NPS1 / Chromatin structure-remodeling complex subunit RSC7 / Chromatin structure-remodeling complex protein RSC14 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex protein RSC8 / Chromatin structure-remodeling complex subunit RSC4 / Chromatin structure-remodeling complex subunit RSC9 / Chromatin structure-remodeling complex subunit SFH1 / Chromatin structure-remodeling complex subunit RSC2 ...Chromatin structure-remodeling complex protein RSC6 / Nuclear protein STH1/NPS1 / Chromatin structure-remodeling complex subunit RSC7 / Chromatin structure-remodeling complex protein RSC14 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex protein RSC8 / Chromatin structure-remodeling complex subunit RSC4 / Chromatin structure-remodeling complex subunit RSC9 / Chromatin structure-remodeling complex subunit SFH1 / Chromatin structure-remodeling complex subunit RSC2 / Chromatin structure-remodeling complex protein RSC3 / Chromatin structure-remodeling complex protein RSC58 / High temperature lethal protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer'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.
History
DepositionDec 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 4, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
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


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

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Details

Has ligand of interestN
Has protein modificationN

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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 FIELD
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
8PHENIXmodel refinement
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
Refine-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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