› 6kw3

Electron Microscopy
7.13Å resolution

The ClassA RSC-Nucleosome Complex

Released:
DOI: 10.2210/pdb6kw3/pdb
PDB entry 6kw3 coloured by chain, front view.
PDB entry 6kw3 coloured by chain, side view.
PDB entry 6kw3 coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the RSC complex bound to the nucleosome.
Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen Z
Science 366 838-843 (2019)
PMID: 31672915
Related structures: EMD-0777

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
PDBe Complex ID:
PDB-CPX-120178 (preferred)
Entry contents:
19 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (21 distinct):
Histone H4 Chains: B, R
Molecule details ›
Chains: B, R
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H3.2 Chains: N, Q
Molecule details ›
Chains: N, Q
Length: 136 amino acids
Theoretical weight: 15.42 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H2A type 1 Chains: O, S
Molecule details ›
Chains: O, S
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Nuclear protein STH1/NPS1 Chains: J, W, Y
Molecule details ›
Chains: J, W, Y
Length: 1359 amino acids
Theoretical weight: 156.98 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32597 (Residues: 1-1359; Coverage: 100%)
Gene names: NPS1, STH1, YIL126W
Sequence domains:
Actin-related protein 7 Chain: f
Molecule details ›
Chain: f
Length: 477 amino acids
Theoretical weight: 53.86 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12406 (Residues: 1-477; Coverage: 100%)
Gene names: ARP7, SWP61, YP9367.14, YPR034W
Sequence domains: Actin
Regulator of Ty1 transposition protein 102 Chain: h
Molecule details ›
Chain: h
Length: 157 amino acids
Theoretical weight: 17.82 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53330 (Residues: 1-157; Coverage: 100%)
Gene names: G9378, RTT102, YGR275W
Sequence domains: Rtt102p-like transcription regulator protein
Chromatin structure-remodeling complex subunit RSC7 Chain: F
Molecule details ›
Chain: F
Length: 435 amino acids
Theoretical weight: 49.72 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32832 (Residues: 1-435; Coverage: 100%)
Gene names: NPL6, RSC7, YM9582.16C, YMR091C
Sequence domains: Chromatin remodelling complex Rsc7/Swp82 subunit
Chromatin structure-remodeling complex protein RSC8 Chains: D, H
Molecule details ›
Chains: D, H
Length: 557 amino acids
Theoretical weight: 63.25 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P43609 (Residues: 1-557; Coverage: 100%)
Gene names: RSC8, SWH3, YFR037C
Sequence domains:
Chromatin structure-remodeling complex subunit RSC9 Chain: M
Molecule details ›
Chain: M
Length: 581 amino acids
Theoretical weight: 65.29 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q03124 (Residues: 1-581; Coverage: 100%)
Gene names: RSC9, YM4987.08, YML127W
Chromatin structure-remodeling complex protein RSC6 Chain: I
Molecule details ›
Chain: I
Length: 483 amino acids
Theoretical weight: 54.22 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25632 (Residues: 1-483; Coverage: 100%)
Gene names: RSC6, YCR052W, YCR52W
Chromatin structure-remodeling complex subunit SFH1 Chain: G
Molecule details ›
Chain: G
Length: 426 amino acids
Theoretical weight: 48.83 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06168 (Residues: 1-426; Coverage: 100%)
Gene names: L8543.4, SFH1, YLR321C
Sequence domains: SNF5 / SMARCB1 / INI1
Chromatin structure-remodeling complex protein RSC58 Chain: A
Molecule details ›
Chain: A
Length: 502 amino acids
Theoretical weight: 57.87 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q07979 (Residues: 1-502; Coverage: 100%)
Gene names: RSC58, YLR033W
Sequence domains: Bromodomain
High temperature lethal protein 1 Chain: E
Molecule details ›
Chain: E
Length: 78 amino acids
Theoretical weight: 9.19 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q9URQ5 (Residues: 1-78; Coverage: 100%)
Gene names: DRT1, HTL1, YCR020W-B
Chromatin structure-remodeling complex protein RSC30 Chain: C
Molecule details ›
Chain: C
Length: 883 amino acids
Theoretical weight: 101.45 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38781 (Residues: 1-883; Coverage: 100%)
Gene names: RSC30, YHR056C
Sequence domains: Fungal Zn(2)-Cys(6) binuclear cluster domain
Chromatin structure-remodeling complex protein RSC3 Chain: K
Molecule details ›
Chain: K
Length: 885 amino acids
Theoretical weight: 101.83 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06639 (Residues: 1-885; Coverage: 100%)
Gene names: D9740.13, RSC3, YDR303C
Sequence domains: Fungal Zn(2)-Cys(6) binuclear cluster domain
Chromatin structure-remodeling complex subunit RSC4 Chain: X
Molecule details ›
Chain: X
Length: 625 amino acids
Theoretical weight: 72.37 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02206 (Residues: 1-625; Coverage: 100%)
Gene names: RSC4, YK107, YKR008W
Sequence domains: Bromodomain
Chromatin structure-remodeling complex subunit RSC2 Chain: L
Molecule details ›
Chain: L
Length: 889 amino acids
Theoretical weight: 102.44 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06488 (Residues: 1-889; Coverage: 100%)
Gene names: L9638.1, RSC2, YLR357W
Sequence domains:
Histone H2B 1.1 Chains: P, T
Molecule details ›
Chains: P, T
Length: 126 amino acids
Theoretical weight: 13.93 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Actin-like protein ARP9 Chain: g
Molecule details ›
Chain: g
Length: 467 amino acids
Theoretical weight: 53.13 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q05123 (Residues: 1-467; Coverage: 100%)
Gene names: ARP9, SWP59, YM9973.07, YMR033W
Sequence domains: Actin
DNA 167 Chain: U
Molecule details ›
Chain: U
Length: 167 nucleotides
Theoretical weight: 51.42 KDa
DNA 167 Chain: V
Molecule details ›
Chain: V
Length: 167 nucleotides
Theoretical weight: 51.68 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 7.13Å
Relevant EMDB volumes: EMD-0777
Expression system: Escherichia coli

Quick links

Citations

13 review citations

Principles of nucleosome recognition by chromatin factors and enzymes.
McGinty et al. (2021)
12 more

6 mentions without citation

Chromatin remodelling comes into focus.
Sundaramoorthy et al. (2020)
5 more