Scm3 deposits a (Cse4–H4)2 tetramer onto DNA through a Cse4–H4 dimer intermediate

The assembly of centromeric nucleosomes is mediated by histone variant-specific chaperones. In budding yeast, the centromere-specific histone H3 variant is Cse4, and the histone chaperone Scm3 functions as a Cse4-specific nucleosome assembly factor. Here, we show that Scm3 exhibits specificity for Cse4-H4, but also interacts with major-type H3-H4 and H2A-H2B. Previously published structures of the Scm3 histone complex demonstrate that Scm3 binds only one copy of Cse4-H4. Consistent with this, we show that Scm3 deposits Cse4-H4 through a dimer intermediate onto deoxyribonucleic acid (DNA) to form a (Cse4-H4)2-DNA complex (tetrasome). Scm3-bound Cse4-H4 does not form a tetramer in the absence of DNA. Moreover, we demonstrate that Cse4 and H3 are structurally compatible to be incorporated in the same nucleosome to form heterotypic particles. Our data shed light on the mechanism of Scm3-mediated nucleosome assembly at the centromere.