› 8kd2

Electron Microscopy
3.02Å resolution

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-270597 (preferred)
Entry contents:
8 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (10 distinct):
Histone deacetylase RPD3 Chain: A
Molecule details ›
Chain: A
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
Transcriptional regulatory protein SIN3 Chain: B
Molecule details ›
Chain: B
Length: 1544 amino acids
Theoretical weight: 176.15 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P22579 (Residues: 2-1536; Coverage: 100%)
Gene names: CPE1, GAM2, RPD1, SDI1, SDS16, SIN3, UME4, YOL004W
Sequence domains:
Chromatin modification-related protein EAF3 Chains: D, F
Molecule details ›
Chains: D, F
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: E, G
Molecule details ›
Chains: E, G
Length: 733 amino acids
Theoretical weight: 84.47 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
Histone H3.2 Chains: O, S
Molecule details ›
Chains: O, S
Length: 135 amino acids
Theoretical weight: 15.3 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: P, T
Molecule details ›
Chains: P, T
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: Q, U
Molecule details ›
Chains: Q, U
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: R, V
Molecule details ›
Chains: R, V
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
187bp DNA Chain: X
Molecule details ›
Chain: X
Length: 187 nucleotides
Theoretical weight: 58.08 KDa
187bp DNA Chain: Y
Molecule details ›
Chain: Y
Length: 187 nucleotides
Theoretical weight: 57.4 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.02Å
Relevant EMDB volumes: EMD-37122
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

3 citation in other articles

Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme.
Zhang et al. (2023)
2 more