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TitleCryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 3061, Year 2023
Publish dateMay 27, 2023
AuthorsAvinash B Patel / Jinkang Qing / Kelly H Tam / Sara Zaman / Maria Luiso / Ishwar Radhakrishnan / Yuan He /
PubMed AbstractThe Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA- ...The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors.
External linksNat Commun / PubMed:37244892 / PubMed Central
MethodsEM (single particle)
Resolution3.4 - 3.5 Å
Structure data

EMDB-29875: Rpd3L Lobe II
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-29876: Rpd3L Lobe I
Method: EM (single particle) / Resolution: 3.4 Å

29892

8ga8

EMDB-29892, PDB-8ga8:
Structure of the yeast (HDAC) Rpd3L complex
Method: EM (single particle) / Resolution: 3.5 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • baker's yeast (brewer's yeast)
KeywordsTRANSCRIPTION / HDAC / Silencing / chromatin

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