Fig. 1: Overall structure of the Rpd3S complex bound to the nucleosome in the H3K9 deacetylation state.

a Domain organization of Rpd3S subunits and histones. b Model of assembly and nucleosome recognition of Rpd3S complex in the H3K9 deacetylation state. Two Rco1 subunits and two Eaf3 subunits are indicated. Ume1 is schematically illustrated to connect to Sin3. Two CHDs of Eaf3A/B are illustrated to interact with H3K36me3 tails. c Dyad view (left) and top view (right) of the cryo-EM composite map of the Rpd3S–nucleosome complex in its H3K9 deacetylation state. Two MRG-PHD arms are illustrated with bold contours. d Corresponding views of the cylindrical models are shown. In all maps and models, the subunits are colored as shown in a.