› 8ga8

Electron Microscopy
3.5Å resolution

Structure of the yeast (HDAC) Rpd3L complex

Released:
DOI: 10.2210/pdb8ga8/pdb
PDB entry 8ga8 coloured by chain, front view.
PDB entry 8ga8 coloured by chain, side view.
PDB entry 8ga8 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex.
Patel AB, Qing J, Tam KH, Zaman S, Luiso M, Radhakrishnan I, He Y
OpenAccess logo Nat Commun 14 3061 (2023)
PMID: 37244892
Related structures: EMD-29892

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 decamer (preferred)
PDBe Complex ID:
PDB-CPX-221218 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (8 distinct):
Transcriptional regulatory protein SDS3 Chain: H
Molecule details ›
Chain: H
Length: 327 amino acids
Theoretical weight: 37.69 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40505 (Residues: 1-327; Coverage: 100%)
Gene names: SDS3, YIL084C
Sequence domains: Sds3-like
Transcriptional regulatory protein SIN3 Chains: A, D
Molecule details ›
Chains: A, D
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 SAP30 Chain: J
Molecule details ›
Chain: J
Length: 201 amino acids
Theoretical weight: 23.06 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38429 (Residues: 1-201; Coverage: 100%)
Gene names: SAP30, YM8156.05, YMR263W
Sequence domains: Sin3 binding region of histone deacetylase complex subunit SAP30
Transcriptional regulatory protein PHO23 Chain: L
Molecule details ›
Chain: L
Length: 330 amino acids
Theoretical weight: 37.08 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P50947 (Residues: 1-330; Coverage: 100%)
Gene names: N2205, PHO23, YNL097C
Sequence domains: Inhibitor of growth proteins N-terminal histone-binding
Transcriptional regulatory protein RXT2 Chain: M
Molecule details ›
Chain: M
Length: 430 amino acids
Theoretical weight: 48.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38255 (Residues: 1-430; Coverage: 100%)
Gene names: RAF60, RXT2, YBR0822, YBR095C
Sequence domains: RXT2-like, N-terminal
Transcriptional regulatory protein DEP1 Chain: G
Molecule details ›
Chain: G
Length: 405 amino acids
Theoretical weight: 47.04 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P31385 (Residues: 1-405; Coverage: 100%)
Gene names: DEP1, FUN54, YAL013W
Sequence domains: Sds3-like
Histone deacetylase RPD3 Chains: B, E
Molecule details ›
Chains: B, E
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
Transcriptional regulatory protein RXT3 Chain: K
Molecule details ›
Chain: K
Length: 294 amino acids
Theoretical weight: 33.85 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q07458 (Residues: 1-294; Coverage: 100%)
Gene names: RXT3, YDL076C
Sequence domains: Histone deacetylation protein Rxt3

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-29892

Quick links

Citations

3 citation in other articles

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