8hy0

Electron Microscopy
3.1Å resolution

Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome

Released:
Primary publication:
Structure of histone deacetylase complex Rpd3S bound to nucleosome.
Nat Struct Mol Biol (2023)
PMID: 37798513
Related structures: EMD-35084

Function and Biology Details

Reaction catalysed:
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-240141 (preferred)
Entry contents:
8 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (10 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.33 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
Transcriptional regulatory protein SIN3 Chain: K
Molecule details ›
Chain: K
Length: 1536 amino acids
Theoretical weight: 175.05 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P22579 (Residues: 1-1536; Coverage: 100%)
Gene names: CPE1, GAM2, RPD1, SDI1, SDS16, SIN3, UME4, YOL004W
Sequence domains:
Histone deacetylase RPD3 Chain: L
Molecule details ›
Chain: L
Length: 433 amino acids
Theoretical weight: 48.96 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P32561 (Residues: 1-433; Coverage: 100%)
Gene names: MOF6, N0305, REC3, RPD3, SDI2, SDS6, YNL330C
Sequence domains: Histone deacetylase domain
Chromatin modification-related protein EAF3 Chains: M, O
Molecule details ›
Chains: M, O
Length: 401 amino acids
Theoretical weight: 45.27 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q12432 (Residues: 1-401; Coverage: 100%)
Gene names: EAF3, YP9367.03C, YPR023C
Sequence domains:
Transcriptional regulatory protein RCO1 Chains: N, P
Molecule details ›
Chains: N, P
Length: 684 amino acids
Theoretical weight: 78.95 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q04779 (Residues: 1-684; Coverage: 100%)
Gene names: RCO1, YM9916.14, YMR075W
Sequence domains: PHD-finger
DNA (352-MER) Chain: I
Molecule details ›
Chain: I
Length: 352 nucleotides
Theoretical weight: 108.34 KDa
DNA (352-MER) Chain: J
Molecule details ›
Chain: J
Length: 352 nucleotides
Theoretical weight: 109.08 KDa

Ligands and Environments

1 bound ligand:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-35084
Expression systems:
  • Escherichia coli
  • Trichoplusia ni