› 8w9c

Electron Microscopy
3.3Å resolution

Cryo-EM structure of the Rpd3S complex from budding yeast

Released:
DOI: 10.2210/pdb8w9c/pdb
PDB entry 8w9c coloured by chain, front view.
PDB entry 8w9c coloured by chain, side view.
PDB entry 8w9c coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structures and dynamics of Rpd3S complex bound to nucleosome.
Wang C, Chu C, Guo Z, Zhan X
OpenAccess logo Sci Adv 10 eadk7678 (2024)
PMID: 38598631
Related structures: EMD-37364

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 hexamer (preferred)
PDBe Complex ID:
PDB-CPX-228502 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Transcriptional regulatory protein SIN3 Chain: A
Molecule details ›
Chain: A
Length: 1536 amino acids
Theoretical weight: 175.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22579 (Residues: 1-1536; Coverage: 100%)
Gene names: CPE1, GAM2, RPD1, SDI1, SDS16, SIN3, UME4, YOL004W
Sequence domains:
Transcriptional regulatory protein RCO1 Chains: E, F
Molecule details ›
Chains: E, F
Length: 684 amino acids
Theoretical weight: 78.95 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04779 (Residues: 1-684; Coverage: 100%)
Gene names: RCO1, YM9916.14, YMR075W
Sequence domains: PHD-finger
Histone deacetylase RPD3 Chain: B
Molecule details ›
Chain: B
Length: 433 amino acids
Theoretical weight: 48.96 KDa
Source organism: Saccharomyces cerevisiae
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: C, D
Molecule details ›
Chains: C, D
Length: 401 amino acids
Theoretical weight: 45.27 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12432 (Residues: 1-401; Coverage: 100%)
Gene names: EAF3, YP9367.03C, YPR023C
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 7 x ZN
Ligand K 2 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-37364

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