› 6z2k

Electron Microscopy
4.5Å resolution

The structure of the tetrameric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex

Released:
DOI: 10.2210/pdb6z2k/pdb
PDB entry 6z2k coloured by chain, front view.
PDB entry 6z2k coloured by chain, side view.
PDB entry 6z2k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure.
Turnbull RE, Fairall L, Saleh A, Kelsall E, Morris KL, Ragan TJ, Savva CG, Chandru A, Millard CJ, Makarova OV, Smith CJ, Roseman AM, Fry AM, Cowley SM, Schwabe JWR
Nat Commun 11 3252 (2020)
PMID: 32591534
Related structures: EMD-11042

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 dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-171751 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Histone deacetylase 1 Chains: C, E, I, K
Molecule details ›
Chains: C, E, I, K
Length: 482 amino acids
Theoretical weight: 55.18 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q13547 (Residues: 1-482; Coverage: 100%)
Gene names: HDAC1, RPD3L1
Sequence domains: Histone deacetylase domain
Deoxynucleotidyltransferase terminal-interacting protein 1 Chains: A, B, G, H
Molecule details ›
Chains: A, B, G, H
Length: 130 amino acids
Theoretical weight: 14.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9H147 (Residues: 1-130; Coverage: 40%)
Gene names: C20orf167, DNTTIP1, TDIF1
Sequence domains: DNTTIP1 dimerisation domain
Mitotic deacetylase-associated SANT domain protein Chains: D, F, J, L
Molecule details ›
Chains: D, F, J, L
Length: 173 amino acids
Theoretical weight: 19.79 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q6PJG2 (Residues: 717-887; Coverage: 16%)
Gene names: C14orf117, C14orf43, ELMSAN1, MIDEAS
Sequence domains: ELM2 domain

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand K 8 x K
Ligand IHP 4 x IHP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.5Å
Relevant EMDB volumes: EMD-11042
Expression system: Homo sapiens

Quick links

Citations

4 review citations

Structure-Based Inhibitor Discovery of Class I Histone Deacetylases (HDACs).
Luo et al. (2020)
3 more

1 mention without citation

Distinct biochemical properties of the class I histone deacetylase complexes.
Lee et al. (2022)