› 8i03

Electron Microscopy
3.2Å resolution

Cryo-EM structure of the SIN3L complex from S. pombe

Released:
DOI: 10.2210/pdb8i03/pdb
PDB entry 8i03 coloured by chain, front view.
PDB entry 8i03 coloured by chain, side view.
PDB entry 8i03 coloured by chain, top view.
Source organism: Schizosaccharomyces pombe
Primary publication:
Two assembly modes for SIN3 histone deacetylase complexes.
Wang C, Guo Z, Chu C, Lu Y, Zhang X, Zhan X
OpenAccess logo Cell Discov 9 42 (2023)
PMID: 37076472
Related structures: EMD-35093

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 undecamer (preferred)
PDBe Complex ID:
PDB-CPX-215113 (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (9 distinct):
Paired amphipathic helix protein pst1 Chain: A
Molecule details ›
Chain: A
Length: 1522 amino acids
Theoretical weight: 171.67 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q09750 (Residues: 1-1522; Coverage: 100%)
Gene names: SPBC12C2.10c, SPBC21D10.01c, pst1
Sequence domains:
Paired amphipathic helix protein pst3 Chain: B
Molecule details ›
Chain: B
Length: 1154 amino acids
Theoretical weight: 133.05 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O74755 (Residues: 1-1154; Coverage: 100%)
Gene names: SPBC1734.16c, pst3
Sequence domains:
Histone deacetylase clr6 Chains: C, D
Molecule details ›
Chains: C, D
Length: 405 amino acids
Theoretical weight: 46.17 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O59702 (Residues: 1-405; Coverage: 100%)
Gene names: SPBC36.05c, clr6
Sequence domains: Histone deacetylase domain
Transcriptional regulatory protein dep1 Chain: E
Molecule details ›
Chain: E
Length: 491 amino acids
Theoretical weight: 55.7 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9P7M1 (Residues: 1-491; Coverage: 100%)
Gene names: SPBC21C3.02c, dep1
Sequence domains: Sds3-like
Transcriptional regulatory protein rxt2 Chain: F
Molecule details ›
Chain: F
Length: 240 amino acids
Theoretical weight: 27.43 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94355 (Residues: 1-240; Coverage: 100%)
Gene names: SPBC428.06c, rtx2
Sequence domains: RXT2-like, N-terminal
Transcriptional regulatory protein sds3 Chain: G
Molecule details ›
Chain: G
Length: 267 amino acids
Theoretical weight: 30.8 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: Q9UTB6 (Residues: 1-267; Coverage: 100%)
Gene names: SPAC25B8.02, sds3
Sequence domains: Sds3-like
Chromatin modification-related protein png2 Chain: H
Molecule details ›
Chain: H
Length: 305 amino acids
Theoretical weight: 34.93 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O74736 (Residues: 1-305; Coverage: 100%)
Gene names: SPBC1709.11c, png2
Sequence domains: Inhibitor of growth proteins N-terminal histone-binding
Transcriptional regulatory protein rxt3 Chain: I
Molecule details ›
Chain: I
Length: 351 amino acids
Theoretical weight: 39.46 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O94707 (Residues: 1-351; Coverage: 100%)
Gene names: SPCC1259.07, rxt3
Sequence domains: Histone deacetylation protein Rxt3
RbAp48-related WD40 repeat-containing protein prw1 Chains: J, K
Molecule details ›
Chains: J, K
Length: 431 amino acids
Theoretical weight: 48.53 KDa
Source organism: Schizosaccharomyces pombe
UniProt:
  • Canonical: O14021 (Residues: 1-431; Coverage: 100%)
Gene names: SPAC29A4.18, prw1
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand K 4 x K
1 modified residue:
Ligand SEP 4 x SEP

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-35093

Quick links

Citations

5 citation in other articles

Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.
Dong et al. (2023)
4 more

1 mention without citation

Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders.
Orenbuch et al. (2023)