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› 9c9g

Electron Microscopy
2.91Å resolution

S.c INO80 in complex with S.c 0/80 nucleosome

Released:
DOI: 10.2210/pdb9c9g/pdb
PDB entry 9c9g coloured by chain, front view.
PDB entry 9c9g coloured by chain, side view.
PDB entry 9c9g coloured by chain, top view.
Source organisms:
Primary publication:
Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning
Kaur U, Wu H, Cheng Y, Narlikar GJ
Science (2025)
Related structures: EMD-45361

Function and Biology Details

Reaction catalysed: 
[ATP + H2O = ADP + phosphate + H(+)., ATP + H2O = ADP + phosphate + H(+)., ATP + H2O = ADP + phosphate + H(+)., ATP + H2O = ADP + phosphate + H(+)., ATP + H2O = ADP + phosphate + H(+)., ATP + H2O = ADP + phosphate + H(+).]
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
PDBe Complex ID:
PDB-CPX-307656 (preferred)
Entry contents:
10 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (12 distinct):
Histone H3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.39 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P61830 (Residues: 1-136; Coverage: 100%)
Gene names: HHT1, HHT2, N2749, SIN2, YBR010W, YBR0201, YNL031C
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H2A.1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 132 amino acids
Theoretical weight: 14.01 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P04911 (Residues: 1-132; Coverage: 100%)
Gene names: H2A1, HTA1, SPT11, YD9934.10, YDR225W
Sequence domains:
Histone H2B.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 131 amino acids
Theoretical weight: 14.28 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P02293 (Residues: 1-131; Coverage: 100%)
Gene names: H2B1, HTB1, SPT12, YD9934.09C, YDR224C
Sequence domains: Core histone H2A/H2B/H3/H4
Chromatin-remodeling ATPase INO80 Chain: Q
Molecule details ›
Chain: Q
Length: 1489 amino acids
Theoretical weight: 171.69 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53115 (Residues: 1-1489; Coverage: 100%)
Gene names: G1880, INO80, YGL150C
Sequence domains:
Actin-related protein 5 Chain: R
Molecule details ›
Chain: R
Length: 755 amino acids
Theoretical weight: 87.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53946 (Residues: 1-755; Coverage: 100%)
Gene names: ARP5, N2430, YNL059C, YNL2430C
Sequence domains: Actin
Chromatin-remodeling complex subunit IES6 Chain: S
Molecule details ›
Chain: S
Length: 166 amino acids
Theoretical weight: 18.56 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32617 (Residues: 1-166; Coverage: 100%)
Gene names: IES6, SYGP-ORF13, YEL044W
Sequence domains: YL1 nuclear protein C-terminal domain
RuvB-like protein 1 Chains: T, V, X
Molecule details ›
Chains: T, V, X
Length: 463 amino acids
Theoretical weight: 50.52 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03940 (Residues: 1-463; Coverage: 100%)
Gene names: RVB1, TIH1, TIP49A, YDR190C
Sequence domains:
RuvB-like protein 2 Chains: U, W, Y
Molecule details ›
Chains: U, W, Y
Length: 471 amino acids
Theoretical weight: 51.67 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12464 (Residues: 1-471; Coverage: 100%)
Gene names: P1060, RVB2, TIH2, TIP49B, YPL235W
Sequence domains:
Ino eighty subunit 2 Chain: Z
Molecule details ›
Chain: Z
Length: 320 amino acids
Theoretical weight: 36.21 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40154 (Residues: 1-320; Coverage: 100%)
Gene names: IES2, N1315, YNL215W
Sequence domains: PAPA-1-like conserved region
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
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
DNA (227-MER) Chain: J
Molecule details ›
Chain: J
Length: 227 nucleotides
Theoretical weight: 70.35 KDa
DNA (227-MER) Chain: I
Molecule details ›
Chain: I
Length: 227 nucleotides
Theoretical weight: 69.84 KDa

Ligands and Environments

1 bound ligand:
Ligand ADP 6 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.91Å
Relevant EMDB volumes: EMD-45361
Expression system: Escherichia coli

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