› 6tda

Electron Microscopy
15Å resolution

Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome

Released:
DOI: 10.2210/pdb6tda/pdb
PDB entry 6tda coloured by chain, front view.
PDB entry 6tda coloured by chain, side view.
PDB entry 6tda coloured by chain, top view.
Source organisms:
Primary publication:
Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome.
Wagner FR, Dienemann C, Wang H, Stützer A, Tegunov D, Urlaub H, Cramer P
Nature 579 448-451 (2020)
PMID: 32188943
Related structures: EMD-10465

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 23-mer (preferred)
PDBe Complex ID:
PDB-CPX-120647 (preferred)
Entry contents:
17 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (19 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Chromatin structure-remodeling complex subunit SFH1 Chain: K
Molecule details ›
Chain: K
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 RSC8 Chain: L
Molecule details ›
Chain: L
Length: 1114 amino acids
Theoretical weight: 126.49 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 RSC7 Chain: M
Molecule details ›
Chain: M
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 subunit RSC9 Chain: N
Molecule details ›
Chain: N
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: O
Molecule details ›
Chain: O
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 protein RSC58 Chain: P
Molecule details ›
Chain: P
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: Q
Molecule details ›
Chain: Q
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 subunit RSC4 Chain: R
Molecule details ›
Chain: R
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
Nuclear protein STH1/NPS1 Chain: S
Molecule details ›
Chain: S
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: T
Molecule details ›
Chain: T
Length: 477 amino acids
Theoretical weight: 54.61 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12406 (Residues: 1-477; Coverage: 100%)
Gene names: ARP7, SWP61, YP9367.14, YPR034W
Sequence domains: Actin
Actin-like protein ARP9 Chain: U
Molecule details ›
Chain: U
Length: 467 amino acids
Theoretical weight: 53.37 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q05123 (Residues: 1-467; Coverage: 100%)
Gene names: ARP9, SWP59, YM9973.07, YMR033W
Sequence domains: Actin
Regulator of Ty1 transposition protein 102 Chain: V
Molecule details ›
Chain: V
Length: 157 amino acids
Theoretical weight: 18.01 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
Unknown protein Chain: X
Molecule details ›
Chain: X
Length: 383 amino acids
Theoretical weight: 32.61 KDa
Source organism: Saccharomyces cerevisiae S288C
DNA-I Chain: I
Molecule details ›
Chain: I
Length: 237 nucleotides
Theoretical weight: 72.88 KDa
DNA-J Chain: J
Molecule details ›
Chain: J
Length: 237 nucleotides
Theoretical weight: 73.48 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
1 modified residue:
Ligand MSE 25 x MSE

Experiments and Validation Details

Entry percentile scores
Resolution: 15Å
Relevant EMDB volumes: EMD-10465
Expression system: Escherichia coli

Quick links

Citations

10 review citations

INO80 and SWR1 complexes: the non-identical twins of chromatin remodelling.
Willhoft et al. (2020)
9 more

13 mentions without citation

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