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- PDB-6kw5: The ClassC RSC-Nucleosome Complex -

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Basic information

Entry
Database: PDB / ID: 6kw5
TitleThe ClassC 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 / 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 mobilization / nucleosome disassembly / UV-damage excision repair ...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 mobilization / nucleosome disassembly / UV-damage excision repair / nucleosome positioning / SWI/SNF complex / NuA4 histone acetyltransferase complex / sister chromatid cohesion / ATP-dependent chromatin remodeling / rRNA transcription / sporulation resulting in formation of a cellular spore / chromosome, centromeric region / histone H4 acetylation / ATPase activity, acting on DNA / transcription elongation from RNA polymerase II promoter / cytoskeleton organization / positive regulation of transcription elongation from RNA polymerase II promoter / meiotic cell cycle / DNA-templated transcription, initiation / chromosome segregation / lysine-acetylated histone binding / nucleosome / double-strand break repair via homologous recombination / base-excision repair / 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 / chromatin organization / 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 / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / regulation of transcription, DNA-templated / structural molecule 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 / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Histone H2A, C-terminal domain / SMARCC, C-terminal / Snf2, ATP coupling 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 ...Rtt102p-like transcription regulator protein / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Histone H2A, C-terminal domain / SMARCC, C-terminal / Snf2, ATP coupling 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 / Histone-fold / CENP-T/Histone H4, histone fold / Homeobox-like domain superfamily / SWIRM domain / Histone H2A/H2B/H3 / SNF5/SMARCB1/INI1 / TATA box binding protein associated factor (TAF) / DNA-binding RFX-type winged-helix domain / Histone H2A / Histone H4 / Helicase, C-terminal / Bromodomain / Zn(2)-C6 fungal-type DNA-binding domain / Bromo adjacent homology (BAH) domain / Histone H2A conserved site / Rsc1/Rsc2, bromodomain / Histone H2B / SWIRM domain / Actin / Centromere kinetochore component CENP-T histone fold / 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 / Zinc finger, ZZ type / Winged helix-like DNA-binding domain superfamily / Myb-like DNA-binding domain / Fungal Zn(2)-Cys(6) binuclear cluster domain / Bromodomain / Bromo adjacent homology (BAH) domain superfamily / Zinc finger, ZZ-type superfamily / ATPase, nucleotide binding domain / 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 / SANT/Myb domain / Actin family / Zinc finger, ZZ-type / Histone H3/CENP-A / SNF2-related domain
Actin-related protein 7 / High temperature lethal protein 1 / Histone H4 / Histone H4 / Histone H2A type 1 / Chromatin structure-remodeling complex protein RSC6 / Chromatin structure-remodeling complex subunit RSC7 / Chromatin structure-remodeling complex protein RSC30 / Chromatin structure-remodeling complex protein RSC8 / Regulator of Ty1 transposition protein 102 ...Actin-related protein 7 / High temperature lethal protein 1 / Histone H4 / Histone H4 / Histone H2A type 1 / Chromatin structure-remodeling complex protein RSC6 / 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 H3.2 / Histone H2A / Chromatin structure-remodeling complex subunit RSC4 / Chromatin structure-remodeling complex subunit RSC9 / 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 / Nuclear protein STH1/NPS1
Biological speciesXenopus laevis (African clawed frog)
Saccharomyces cerevisiae (baker's yeast)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.13 Å
AuthorsYe, Y.P. / Wu, H. / Chen, K.J. / Verma, N. / Cairns, B. / Gao, N. / Chen, Z.C.
CitationJournal: To Be Published
Title: Structure of the RSC complex bound to the nucleosome
Authors: Ye, Y.P. / Wu, H. / Chen, K.J. / Verma, N. / Cairns, B. / Gao, N. / Chen, Z.C.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release

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Assembly

Deposited unit
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
W: Histone H4
f: Actin-related protein 7
h: Regulator of Ty1 transposition protein 102
R: Histone H3.2
S: Histone H4
T: Histone H2A
V: Histone H3.2
O: Histone H2A
U: Histone H4
Y: Histone H4
g: Actin-like protein ARP9
B: DNA 167
N: DNA 167
P: Nuclear protein STH1/NPS1
Q: 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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Chromatin structure-remodeling complex subunit ... , 5 types, 5 molecules FMGXL

#1: 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
#3: 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
#5: 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
#11: 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
#12: 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

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

#2: Protein 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
#4: 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
#6: 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
#9: 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
#10: Protein 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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Protein , 9 types, 15 molecules JPQEWSfhRVTOUYg

#7: Protein 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
#8: 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
#13: Protein 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
#14: Protein 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
#15: Protein 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
#16: Protein 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
#17: Protein 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
#18: Protein 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
#19: Protein 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 BN

#20: DNA chain DNA 167


Mass: 51421.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#21: 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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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-#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: 10.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24146 / Symmetry type: POINT

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