Crystal Structure of the Yeast Inner Kinetochore Subunit Cep3p

SummaryIn budding yeast, the four-protein CBF3 complex (Skp1p-Ctf13p-Cep3p-Ndc10p) initiates kinetochore assembly by binding to the CDEIII locus of centromeric DNA. A Cep3p dimer recruits a Skp1p-Ctf13p heterodimer and contacts two sites on CDEIII. We report here the crystal structure, determined at 2.8 Å resolution by multiple isomorphous replacement with anomalous scattering, of a truncated Cep3p (Cep3p [47–608]), comprising all but an N-terminal, Zn2Cys6-cluster, DNA-binding module. Cep3p has a well-ordered structure throughout essentially all of its polypeptide chain, unlike most yeast transcription factors, including those with Zn2Cys6 clusters, such as Gal4p. This difference may reflect an underlying functional distinction: whereas any particular transcription factor must adapt to a variety of upstream activating sites, Cep3p scaffolds kinetochore assembly on centromeres uniformly configured on all 16 yeast chromosomes. We have, using the structure of Cep3p (47–608) and the known structures of Zn2Cys6-cluster domains, modeled the interaction of Cep3p with CDEIII