› 7yi2

Electron Microscopy
3.4Å resolution

Cryo-EM structure of Rpd3S in loose-state Rpd3S-NCP complex

Released:
DOI: 10.2210/pdb7yi2/pdb
PDB entry 7yi2 coloured by chain, front view.
PDB entry 7yi2 coloured by chain, side view.
PDB entry 7yi2 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Diverse modes of H3K36me3-guided nucleosomal deacetylation by Rpd3S.
Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H
Nature (2023)
PMID: 37468628
Related structures: EMD-33849

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 heptamer (preferred)
PDBe Complex ID:
PDB-CPX-217985 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Transcriptional regulatory protein SIN3 Chain: A
Molecule details ›
Chain: A
Length: 1536 amino acids
Theoretical weight: 175.05 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P22579 (Residues: 1-1536; Coverage: 100%)
Gene names: CPE1, GAM2, RPD1, SDI1, SDS16, SIN3, UME4, YOL004W
Sequence domains:
Histone deacetylase RPD3 Chain: B
Molecule details ›
Chain: B
Length: 433 amino acids
Theoretical weight: 48.96 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
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 Chain: C
Molecule details ›
Chain: C
Length: 401 amino acids
Theoretical weight: 45.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q12432 (Residues: 1-401; Coverage: 100%)
Gene names: EAF3, YP9367.03C, YPR023C
Sequence domains:
Transcriptional regulatory protein RCO1 Chains: D, E
Molecule details ›
Chains: D, E
Length: 684 amino acids
Theoretical weight: 78.95 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q04779 (Residues: 1-684; Coverage: 100%)
Gene names: RCO1, YM9916.14, YMR075W
Sequence domains: PHD-finger
Wisdom 601 DNA (167-MER) Chain: G
Molecule details ›
Chain: G
Length: 167 nucleotides
Theoretical weight: 51.31 KDa
Wisdom 601 DNA (167-MER) Chain: H
Molecule details ›
Chain: H
Length: 167 nucleotides
Theoretical weight: 51.8 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 5 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-33849
Expression system: Spodoptera frugiperda

Quick links

Citations

4 citation in other articles

Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.
Dong et al. (2023)
3 more