› 6z6p

Electron Microscopy
4.43Å 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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
PDBe Complex ID:
PDB-CPX-121003 (preferred)
Entry contents:
12 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (14 distinct):
Histone deacetylase HDA1 Chain: K
Molecule details ›
Chain: K
Length: 661 amino acids
Theoretical weight: 74.85 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P53973 (Residues: 40-700; Coverage: 94%)
Gene names: HDA1, N2819, YNL021W
Sequence domains:
Histone deacetylase HDA1 Chain: L
Molecule details ›
Chain: L
Length: 672 amino acids
Theoretical weight: 76.02 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P53973 (Residues: 29-700; Coverage: 95%)
Gene names: HDA1, N2819, YNL021W
Sequence domains:
HDA1 complex subunit 3 Chain: M
Molecule details ›
Chain: M
Length: 543 amino acids
Theoretical weight: 63.42 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q06623 (Residues: 28-639; Coverage: 83%)
Gene names: HDA3, PLO1, YPR179C
Sequence domains: Class II histone deacetylase complex subunits 2 and 3
HDA1 complex subunit 2 Chain: N
Molecule details ›
Chain: N
Length: 629 amino acids
Theoretical weight: 71.92 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q06629 (Residues: 10-638; Coverage: 93%)
Gene names: HDA2, PLO2, YDR295C
Sequence domains: Class II histone deacetylase complex subunits 2 and 3
Histone H3.2 Chain: A
Molecule details ›
Chain: A
Length: 97 amino acids
Theoretical weight: 11.43 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 39-135; Coverage: 71%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chain: B
Molecule details ›
Chain: B
Length: 83 amino acids
Theoretical weight: 9.41 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 21-103; Coverage: 81%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A Chain: C
Molecule details ›
Chain: C
Length: 103 amino acids
Theoretical weight: 11.29 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6AZJ8 (Residues: 17-119; Coverage: 79%)
Gene names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
Sequence domains:
Histone H2B 1.1 Chain: D
Molecule details ›
Chain: D
Length: 95 amino acids
Theoretical weight: 10.61 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 32-126; Coverage: 75%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H3.2 Chain: E
Molecule details ›
Chain: E
Length: 97 amino acids
Theoretical weight: 11.41 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 40-136; Coverage: 71%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chain: F
Molecule details ›
Chain: F
Length: 78 amino acids
Theoretical weight: 8.8 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 26-103; Coverage: 76%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chain: G
Molecule details ›
Chain: G
Length: 105 amino acids
Theoretical weight: 11.49 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 15-119; Coverage: 81%)
Sequence domains:
Histone H2B 1.1 Chain: H
Molecule details ›
Chain: H
Length: 93 amino acids
Theoretical weight: 10.35 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 33-125; Coverage: 74%)
Sequence domains: Core histone H2A/H2B/H3/H4
DNA (145-MER) Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.52 KDa
DNA (145-MER) Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.99 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 4.43Å
Relevant EMDB volumes: EMD-11102
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Histone deacetylases modulate resistance to the therapy in lung cancer.
Contreras-Sanzón et al. (2022)
2 more

1 mention without citation

Principles of nucleosome recognition by chromatin factors and enzymes.
McGinty et al. (2021)