› 8hpo

Electron Microscopy
2.6Å resolution

Cryo-EM structure of a SIN3/HDAC complex from budding yeast

Released:
DOI: 10.2210/pdb8hpo/pdb
PDB entry 8hpo coloured by chain, front view.
PDB entry 8hpo coloured by chain, side view.
PDB entry 8hpo coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structure of a SIN3-HDAC complex from budding yeast.
Guo Z, Chu C, Lu Y, Zhang X, Xiao Y, Wu M, Gao S, Wong CCL, Zhan X, Wang C
Nat Struct Mol Biol (2023)
PMID: 37081318
Related structures: EMD-34935

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 undecamer (preferred)
PDBe Complex ID:
PDB-CPX-215172 (preferred)
Entry contents:
10 distinct polypeptide molecules
Macromolecules (10 distinct):
Transcriptional regulatory protein UME1 Chain: K
Molecule details ›
Chain: K
Length: 460 amino acids
Theoretical weight: 51.08 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q03010 (Residues: 1-460; Coverage: 100%)
Gene names: LPI7C, UME1, WTM3, YPL139C
Transcriptional regulatory protein SDS3 Chain: D
Molecule details ›
Chain: D
Length: 327 amino acids
Theoretical weight: 37.77 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40505 (Residues: 1-327; Coverage: 100%)
Gene names: SDS3, YIL084C
Sequence domains: Sds3-like
Histone deacetylase RPD3 Chain: F
Molecule details ›
Chain: F
Length: 433 amino acids
Theoretical weight: 49.36 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32561 (Residues: 1-433; Coverage: 100%)
Gene names: MOF6, N0305, REC3, RPD3, SDI2, SDS6, YNL330C
Sequence domains: Histone deacetylase domain
Histone deacetylase RPD3 Chain: G
Molecule details ›
Chain: G
Length: 433 amino acids
Theoretical weight: 48.96 KDa
Source organism: Saccharomyces cerevisiae S288C
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 SAP30 Chain: I
Molecule details ›
Chain: I
Length: 201 amino acids
Theoretical weight: 23.14 KDa
Source organism: Saccharomyces cerevisiae S288C
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 SIN3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 1536 amino acids
Theoretical weight: 175.05 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22579 (Residues: 1-1536; Coverage: 100%)
Gene names: CPE1, GAM2, RPD1, SDI1, SDS16, SIN3, UME4, YOL004W
Sequence domains:
Transcriptional regulatory protein DEP1 Chain: H
Molecule details ›
Chain: H
Length: 405 amino acids
Theoretical weight: 47.04 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P31385 (Residues: 1-405; Coverage: 100%)
Gene names: DEP1, FUN54, YAL013W
Sequence domains: Sds3-like
Transcriptional regulatory protein PHO23 Chain: C
Molecule details ›
Chain: C
Length: 330 amino acids
Theoretical weight: 37.08 KDa
Source organism: Saccharomyces cerevisiae S288C
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: E
Molecule details ›
Chain: E
Length: 430 amino acids
Theoretical weight: 48.84 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38255 (Residues: 1-430; Coverage: 100%)
Gene names: RAF60, RXT2, YBR0822, YBR095C
Sequence domains: RXT2-like, N-terminal
Transcriptional regulatory protein RXT3 Chain: J
Molecule details ›
Chain: J
Length: 294 amino acids
Theoretical weight: 33.85 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q07458 (Residues: 1-294; Coverage: 100%)
Gene names: RXT3, YDL076C
Sequence domains: Histone deacetylation protein Rxt3

Ligands and Environments

3 bound ligands:
Ligand TPO 1 x TPO
Ligand ZN 2 x ZN
Ligand K 4 x K
2 modified residues:
Ligand SEP 5 x SEP
Ligand TPO 4 x TPO

Experiments and Validation Details

Entry percentile scores
Resolution: 2.6Å
Relevant EMDB volumes: EMD-34935

Quick links

Citations

4 citation in other articles

HDAC1: An Essential and Conserved Member of the Diverse Zn2+-Dependent HDAC Family Driven by Divergent Selection Pressure.
Yang et al. (2023)
3 more