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- PDB-6kw3: The ClassA RSC-Nucleosome Complex -

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Basic information

Entry
Database: PDB / ID: 6kw3
TitleThe ClassA RSC-Nucleosome Complex
Components
  • (Chromatin structure-remodeling complex protein ...) x 5
  • (Chromatin structure-remodeling complex subunit ...) x 5
  • (DNA 167) x 2
  • (Histone H4) x 2
  • Actin-like protein ARP9
  • Actin-related protein 7
  • High temperature lethal protein 1
  • Histone H2A
  • Histone H3.2
  • Nuclear protein STH1/NPS1
  • Regulator of Ty1 transposition protein 102
KeywordsDNA BINDING PROTEIN/DNA / chromatin remodeler / SWI/SNF family / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of sporulation resulting in formation of a cellular spore / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / transfer RNA gene-mediated silencing / plasmid maintenance / structural constituent of postsynaptic actin cytoskeleton / DNA translocase activity / nucleosome mobilization / RSC-type complex / nucleosome positioning ...regulation of sporulation resulting in formation of a cellular spore / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / transfer RNA gene-mediated silencing / plasmid maintenance / structural constituent of postsynaptic actin cytoskeleton / DNA translocase activity / nucleosome mobilization / RSC-type complex / nucleosome positioning / UV-damage excision repair / nucleosome disassembly / SWI/SNF complex / NuA4 histone acetyltransferase complex / sister chromatid cohesion / ATP-dependent chromatin remodeling / rRNA transcription / histone H4 acetylation / synaptic vesicle endocytosis / sporulation resulting in formation of a cellular spore / chromosome, centromeric region / DNA-dependent ATPase activity / cytoskeleton organization / transcription elongation from RNA polymerase II promoter / helicase activity / DNA helicase / DNA helicase activity / DNA-templated transcription, initiation / actin filament / lysine-acetylated histone binding / positive regulation of transcription elongation from RNA polymerase II promoter / meiotic cell cycle / chromosome segregation / rRNA processing / chromatin DNA binding / nucleosome / double-strand break repair / double-strand break repair via homologous recombination / cellular response to hydrogen peroxide / base-excision repair / double-strand break repair via nonhomologous end joining / chromatin organization / G2/M transition of mitotic cell cycle / histone binding / transcription regulatory region DNA binding / chromatin remodeling / sequence-specific DNA binding / ATPase activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / cellular response to DNA damage stimulus / chromatin binding / regulation of transcription, DNA-templated / structural molecule activity / protein heterodimerization activity / positive regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus
Rtt102p-like transcription regulator protein / SWIRM domain / P-loop containing nucleoside triphosphate hydrolase / Chromatin structure-remodeling complex subunit RSC1/RSC2/RSC4 / Histone H4, conserved site / Bromodomain, conserved site / Transcription regulator protein Rtt102 / SANT domain / Chromatin-remodeling complex component Sfh1/SNF5 / Helicase/SANT-associated domain ...Rtt102p-like transcription regulator protein / SWIRM domain / P-loop containing nucleoside triphosphate hydrolase / Chromatin structure-remodeling complex subunit RSC1/RSC2/RSC4 / Histone H4, conserved site / Bromodomain, conserved site / Transcription regulator protein Rtt102 / SANT domain / Chromatin-remodeling complex component Sfh1/SNF5 / Helicase/SANT-associated domain / Helicase superfamily 1/2, ATP-binding domain / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Histone-fold / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / SMARCC, C-terminal / SNF5/SMARCB1/INI1 / TATA box binding protein associated factor (TAF) / Actin family / DNA-binding RFX-type winged-helix domain / Histone H2A / Helicase, C-terminal / Bromodomain / Zn(2)-C6 fungal-type DNA-binding domain / Bromo adjacent homology (BAH) domain / SANT/Myb domain / Histone H2B / Zinc finger, ZZ-type / Snf2, ATP coupling domain / Histone H2A, C-terminal domain / Histone H3/CENP-A / Zinc finger, ZZ type / Actin / C-terminus of histone H2A / Core histone H2A/H2B/H3/H4 / BAH domain / Snf2-ATP coupling, chromatin remodelling complex / HSA / Helicase conserved C-terminal domain / SNF2 family N-terminal domain / SNF5 / SMARCB1 / INI1 / Chromatin remodelling complex Rsc7/Swp82 subunit / SWIRM-associated region 1 / SWIRM domain / Myb-like DNA-binding domain / Histone H2A conserved site / Fungal Zn(2)-Cys(6) binuclear cluster domain / Centromere kinetochore component CENP-T histone fold / Bromodomain / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / SNF2-like, N-terminal domain superfamily / Remodelling complex subunit Rsc/polybromo / SWIB/MDM2 domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Bromodomain-like superfamily / Winged helix-like DNA-binding domain superfamily / Rsc1/Rsc2, bromodomain / CENP-T/Histone H4, histone fold / SNF2-related, N-terminal domain / Histone H4
Histone H4 / Chromatin structure-remodeling complex protein RSC6 / Histone H2B 1.1 / Nuclear protein STH1/NPS1 / Chromatin structure-remodeling complex subunit RSC4 / Chromatin structure-remodeling complex subunit RSC7 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex protein RSC8 / Regulator of Ty1 transposition protein 102 / Histone H4 ...Histone H4 / Chromatin structure-remodeling complex protein RSC6 / Histone H2B 1.1 / Nuclear protein STH1/NPS1 / Chromatin structure-remodeling complex subunit RSC4 / Chromatin structure-remodeling complex subunit RSC7 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex protein RSC8 / Regulator of Ty1 transposition protein 102 / Histone H4 / Histone H2A type 1 / Chromatin structure-remodeling complex subunit RSC9 / High temperature lethal protein 1 / Actin-like protein ARP9 / Chromatin structure-remodeling complex subunit SFH1 / Chromatin structure-remodeling complex subunit RSC2 / Chromatin structure-remodeling complex protein RSC3 / Chromatin structure-remodeling complex protein RSC58 / Actin-related protein 7 / Histone H2A / Histone H3.2
Biological speciesXenopus laevis (African clawed frog)
Saccharomyces cerevisiae (baker's yeast)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.13 Å
AuthorsYe, Y.P. / Wu, H. / Chen, K.J. / Verma, N. / Cairns, B. / Gao, N. / Chen, Z.C.
CitationJournal: Science / Year: 2019
Title: Structure of the RSC complex bound to the nucleosome.
Authors: Youpi Ye / Hao Wu / Kangjing Chen / Cedric R Clapier / Naveen Verma / Wenhao Zhang / Haiteng Deng / Bradley R Cairns / Ning Gao / Zhucheng Chen /
Abstract: The RSC complex remodels chromatin structure and regulates gene transcription. We used cryo-electron microscopy to determine the structure of yeast RSC bound to the nucleosome. RSC is delineated into ...The RSC complex remodels chromatin structure and regulates gene transcription. We used cryo-electron microscopy to determine the structure of yeast RSC bound to the nucleosome. RSC is delineated into the adenosine triphosphatase motor, the actin-related protein module, and the substrate recruitment module (SRM). RSC binds the nucleosome mainly through the motor, with the auxiliary subunit Sfh1 engaging the H2A-H2B acidic patch to enable nucleosome ejection. SRM is organized into three substrate-binding lobes poised to bind their respective nucleosomal epitopes. The relative orientations of the SRM and the motor on the nucleosome explain the directionality of DNA translocation and promoter nucleosome repositioning by RSC. Our findings shed light on RSC assembly and functionality, and they provide a framework to understand the mammalian homologs BAF/PBAF and the Sfh1 ortholog INI1/BAF47, which are frequently mutated in cancers.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
B: Histone H4
N: Histone H3.2
O: Histone H2A
Q: Histone H3.2
R: Histone H4
S: Histone H2A
U: DNA 167
V: DNA 167
W: Nuclear protein STH1/NPS1
f: Actin-related protein 7
h: Regulator of Ty1 transposition protein 102
F: Chromatin structure-remodeling complex subunit RSC7
H: Chromatin structure-remodeling complex protein RSC8
D: Chromatin structure-remodeling complex protein RSC8
M: Chromatin structure-remodeling complex subunit RSC9
I: Chromatin structure-remodeling complex protein RSC6
G: Chromatin structure-remodeling complex subunit SFH1
A: Chromatin structure-remodeling complex protein RSC58
J: Nuclear protein STH1/NPS1
E: High temperature lethal protein 1
C: Chromatin structure-remodeling complex protein RSC30
K: Chromatin structure-remodeling complex protein RSC3
X: Chromatin structure-remodeling complex subunit RSC4
L: Chromatin structure-remodeling complex subunit RSC2
T: Histone H4
P: Histone H4
g: Actin-like protein ARP9
Y: Nuclear protein STH1/NPS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,598,36329
Polymers1,598,29728
Non-polymers651
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 9 types, 15 molecules BRNQOSWJYfhETPg

#1: Protein/peptide Histone H4 /


Mass: 11394.426 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
#2: Protein/peptide Histone H3.2


Mass: 15421.101 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
#3: Protein/peptide Histone H2A /


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#6: Protein/peptide Nuclear protein STH1/NPS1 / ATP-dependent helicase STH1 / Chromatin structure-remodeling complex protein STH1 / SNF2 homolog


Mass: 156982.406 Da / Num. of mol.: 3 / 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
#7: Protein/peptide Actin-related protein 7 / Actin-like protein ARP7 / Chromatin structure-remodeling complex protein ARP7 / SWI/SNF complex component ARP7


Mass: 53863.016 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: Q12406
#8: Protein/peptide Regulator of Ty1 transposition protein 102


Mass: 17817.615 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: P53330
#15: Protein/peptide 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
#20: Protein/peptide Histone H4 /


Mass: 13925.202 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18028549mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L8G0X3, UniProt: P02281*PLUS
#21: Protein/peptide Actin-like protein ARP9 / Chromatin structure-remodeling complex protein ARP9 / SWI/SNF complex component ARP9


Mass: 53131.930 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: Q05123

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DNA chain , 2 types, 2 molecules UV

#4: DNA chain DNA 167


Mass: 51421.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA 167


Mass: 51683.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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

#9: Protein/peptide 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
#11: Protein/peptide 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
#13: Protein/peptide 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
#18: Protein/peptide 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
#19: Protein/peptide 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

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Chromatin structure-remodeling complex protein ... , 5 types, 6 molecules HDIACK

#10: Protein/peptide Chromatin structure-remodeling complex protein RSC8 / Remodel the structure of chromatin complex subunit 8 / SWI3 homolog


Mass: 63253.965 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 / References: UniProt: P43609
#12: Protein/peptide 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
#14: Protein/peptide 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
#16: Protein/peptide 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
#17: Protein/peptide Chromatin structure-remodeling complex protein RSC3 / Remodel the structure of chromatin complex subunit 3


Mass: 101833.961 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

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Non-polymers , 1 types, 1 molecules

#22: 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: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RSC / Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 7.5
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: SPOT SCAN
Electron lensMode: DARK FIELD
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45077 / Symmetry type: POINT

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