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TitleStructure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 8128, Year 2023
Publish dateDec 8, 2023
AuthorsJonathan W Markert / Seychelle M Vos / Lucas Farnung /
PubMed AbstractAcetylation of histones is a key post-translational modification that guides gene expression regulation. In yeast, the class I histone deacetylase containing Rpd3S complex plays a critical role in ...Acetylation of histones is a key post-translational modification that guides gene expression regulation. In yeast, the class I histone deacetylase containing Rpd3S complex plays a critical role in the suppression of spurious transcription by removing histone acetylation from actively transcribed genes. The S. cerevisiae Rpd3S complex has five subunits (Rpd3, Sin3, Rco1, Eaf3, and Ume1) but its subunit stoichiometry and how the complex engages nucleosomes to achieve substrate specificity remains elusive. Here we report the cryo-EM structure of the complete Rpd3S complex bound to a nucleosome. Sin3 and two copies of subunits Rco1 and Eaf3 encircle the deacetylase subunit Rpd3 and coordinate the positioning of Ume1. The Rpd3S complex binds both trimethylated H3 tails at position lysine 36 and makes multiple additional contacts with the nucleosomal DNA and the H2A-H2B acidic patch. Direct regulation via the Sin3 subunit coordinates binding of the acetylated histone substrate to achieve substrate specificity.
External linksNat Commun / PubMed:38065958 / PubMed Central
MethodsEM (single particle)
Resolution2.8 Å
Structure data

41449

8tof

EMDB-41449, PDB-8tof:
Rpd3S bound to an H3K36Cme3 modified nucleosome
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • xenopus laevis (African clawed frog)
  • synthetic construct (others)
KeywordsTRANSCRIPTION/DNA / nucleosome / methylation / acetylation / Rpd3S / TRANSCRIPTION / TRANSCRIPTION-DNA complex

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