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Schizosaccharomyces pombe Clr6S, a class I histone deacetylase complex, functions as a zinc-dependent enzyme to remove acetyl groups from lysine residues in histone tails. We report here the cryo-EM structures of Clr6S alone and in a complex with a nucleosome. The active center, revealed at near atomic resolution, includes features important for catalysis - a water molecule coordinated by zinc, the likely nucleophile for attack on the acetyl-lysine bond, and a loop that may position the substrate for catalysis. The cryo-EM map in the presence of a nucleosome reveals multiple Clr6S-nucleosome contacts, and a high degree of relative motion of Clr6S and the nucleosome. Such flexibility may be attributed to interaction at a site in the flexible histone tail, and is likely important for function of the deacetylase, which acts at multiple sites in other histone tails.