8ifg

Electron Microscopy
3.2Å resolution

Cryo-EM structure of the Clr6S (Clr6-HDAC) complex from S. pombe

Released:
Primary publication:
Class I histone deacetylase complex: Structure and functional correlates.
Proc Natl Acad Sci U S A 120 e2307598120 (2023)
PMID: 37459529
Related structures: EMD-35416

Function and Biology Details

Reaction catalysed:
Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
PDBe Complex ID:
PDB-CPX-215112 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
RbAp48-related WD40 repeat-containing protein prw1 Chain: B
Molecule details ›
Chain: B
Length: 431 amino acids
Theoretical weight: 48.53 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O14021 (Residues: 1-431; Coverage: 100%)
Gene names: SPAC29A4.18, prw1
Sequence domains:
Paired amphipathic helix protein pst2 Chain: A
Molecule details ›
Chain: A
Length: 1075 amino acids
Theoretical weight: 125.01 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O13919 (Residues: 1-1075; Coverage: 100%)
Gene names: SPAC23C11.15, pst2
Sequence domains:
Histone deacetylase clr6 Chain: C
Molecule details ›
Chain: C
Length: 401 amino acids
Theoretical weight: 45.77 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O59702 (Residues: 5-405; Coverage: 99%)
Gene names: SPBC36.05c, clr6
Sequence domains: Histone deacetylase domain
Chromatin modification-related protein eaf3 Chains: D, E
Molecule details ›
Chains: D, E
Length: 337 amino acids
Theoretical weight: 39.19 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O13953 (Residues: 1-337; Coverage: 100%)
Gene names: SPAC23H4.12, alp13, eaf3
Sequence domains:
Cph1 Chain: F
Molecule details ›
Chain: F
Length: 404 amino acids
Theoretical weight: 45.05 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q09819 (Residues: 1-404; Coverage: 100%)
Gene name: SPAC16C9.05
Sequence domains: PHD-finger
Cph2 Chain: P
Molecule details ›
Chain: P
Length: 607 amino acids
Theoretical weight: 68.87 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q09698 (Residues: 1-607; Coverage: 100%)
Gene name: SPAC2F7.07c
Sequence domains: PHD-finger

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-35416
Expression system: Trichoplusia ni