› 8kd4

Electron Microscopy
2.93Å resolution

Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1

Released:
DOI: 10.2210/pdb8kd4/pdb
PDB entry 8kd4 coloured by chain, front view.
PDB entry 8kd4 coloured by chain, side view.
PDB entry 8kd4 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
OpenAccess logo Cell Res (2023)
PMID: 37666978
Related structures: EMD-37124

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-270598 (preferred)
Entry contents:
8 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (10 distinct):
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:
Histone H3.2 Chains: O, S
Molecule details ›
Chains: O, S
Length: 135 amino acids
Theoretical weight: 15.31 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
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: 1371 amino acids
Theoretical weight: 157.59 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P22579 (Residues: 215-1536; Coverage: 86%)
Gene names: CPE1, GAM2, RPD1, SDI1, SDS16, SIN3, UME4, YOL004W
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
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

1 bound ligand:
Ligand ZN 1 x ZN
1 modified residue:
Ligand M3L 2 x M3L

Experiments and Validation Details

Entry percentile scores
Resolution: 2.93Å
Relevant EMDB volumes: EMD-37124
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

2 citation in other articles

Rpd3S meets the nucleosome.
Carrozza et al. (2023)
1 more