8C60 image
Entry Detail
PDB ID:
8C60
EMDB ID:
Keywords:
Title:
Cryo-EM structure of the human SIN3B full-length complex at 3.4 Angstrom resolution
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2023-01-10
Release Date:
2023-05-10
Method Details:
Experimental Method:
Resolution:
3.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Isoform 2 of Paired amphipathic helix protein Sin3b
Chain IDs:A
Chain Length:1130
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone deacetylase 2
Chain IDs:B
Chain Length:488
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:PHD finger protein 12
Chain IDs:C
Chain Length:1004
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Mortality factor 4-like protein 1
Chain IDs:D
Chain Length:362
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex.
Nat Commun 14 2556 2556 (2023)
PMID: 37137925 DOI: 10.1038/s41467-023-38276-0

Abstact

Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing transcription and regulating the transcriptional output of each gene. Although these complexes are drug targets and crucial regulators of organismal physiology, their structure and mechanisms of action are largely unclear. Here, we present the structure of a complete human SIN3B histone deacetylase holo-complex with and without a substrate mimic. Remarkably, SIN3B encircles the deacetylase and contacts its allosteric basic patch thereby stimulating catalysis. A SIN3B loop inserts into the catalytic tunnel, rearranges to accommodate the acetyl-lysine moiety, and stabilises the substrate for specific deacetylation, which is guided by a substrate receptor subunit. Our findings provide a model of specificity for a main transcriptional regulator conserved from yeast to human and a resource of protein-protein interactions for future drug designs.

Legend

Protein

Chemical

Disease

Primary Citation of related structures