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Structure paper

TitleMechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 2556, Year 2023
Publish dateMay 3, 2023
AuthorsMandy S M Wan / Reyhan Muhammad / Marios G Koliopoulos / Theodoros I Roumeliotis / Jyoti S Choudhary / Claudio Alfieri /
PubMed AbstractLysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing ...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.
External linksNat Commun / PubMed:37137925 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 3.7 Å
Structure data

16147

8bpa

EMDB-16147, PDB-8bpa:
Cryo-EM structure of the human SIN3B histone deacetylase complex at 3.7 Angstrom
Method: EM (single particle) / Resolution: 3.7 Å

16148

8bpb

EMDB-16148, PDB-8bpb:
Cryo-EM structure of the human SIN3B histone deacetylase core complex at 2.8 Angstrom
Method: EM (single particle) / Resolution: 2.8 Å

16149

8bpc

EMDB-16149, PDB-8bpc:
Cryo-EM structure of the human SIN3B histone deacetylase core complex with SAHA at 2.8 Angstrom
Method: EM (single particle) / Resolution: 2.8 Å

16449

8c60

EMDB-16449, PDB-8c60:
Cryo-EM structure of the human SIN3B full-length complex at 3.4 Angstrom resolution
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-CA:
Unknown entry

ChemComp-ACT:
ACETATE ION / Acetate

ChemComp-HOH:
WATER / Water

ChemComp-SHH:
OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE

Source
  • homo sapiens (human)
KeywordsGENE REGULATION / HDAC / Chromatin / Cell cycle / transcription / HYDROLASE / Histone deacetylase

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