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Ndc10 is a platform for inner kinetochore assembly in budding yeast

Nature Structural & Molecular Biology volume 19, pages 48–55 (2012)Cite this article

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Abstract

Kinetochores link centromeric DNA to spindle microtubules and ensure faithful chromosome segregation during mitosis. In point-centromere yeasts, the CBF3 complex Skp1–Ctf13–(Cep3)2–(Ndc10)2 recognizes a conserved centromeric DNA element through contacts made by Cep3 and Ndc10. We describe here the five-domain organization of Kluyveromyces lactis Ndc10 and the structure at 2.8 Å resolution of domains I–II (residues 1–402) bound to DNA. The structure resembles tyrosine DNA recombinases, although it lacks both endonuclease and ligase activities. Structural and biochemical data demonstrate that each subunit of the Ndc10 dimer binds a separate fragment of DNA, suggesting that Ndc10 stabilizes a DNA loop at the centromere. We describe in vitro association experiments showing that specific domains of Ndc10 interact with each of the known inner-kinetochore proteins or protein complexes in budding yeast. We propose that Ndc10 provides a central platform for inner-kinetochore assembly.

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Figure 1: Domains of K. lactis Ndc10 and crystal structure of DI–II.
Figure 2: Surface charge distribution and DNA contacts of Ndc10 DI–II.
Figure 3: Structural alignment of K. lactis Ndc10 DI–II with Flp recombinases.
Figure 4: Dimerization of K. lactis Ndc10 DI–III.
Figure 5: Interactions of Ndc10-associated proteins or protein complexes in the inner kinetochore.
Figure 6: Interaction of Ndc10 domain IV–V with N-terminal Scm3.
Figure 7: Schematic model of Ndc10 interactions on budding yeast centromeres.

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Acknowledgements

We thank the staff at the Advanced Photon Source NE-CAT beamlines for advice and assistance with data collection and interpretation, D. King of the Howard Hughes Medical Institute Mass Spectrometry Facility, University of California, Berkeley, for mass spectrometry, and K. Corbett and P. Sorger for helpful discussions. This research was supported by the Howard Hughes Medical Institute.

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  1. Department of Biological Chemistry and Molecular Pharmacology, Jack and Eileen Connors Structural Biology Laboratory and Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA

    Uhn-Soo Cho & Stephen C Harrison

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U.-S.C. designed and conducted experiments, determined and refined the structures, analyzed data and wrote the manuscript; S.C.H directed the project, analyzed data and wrote the manuscript.

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Correspondence to Stephen C Harrison.

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Cho, US., Harrison, S. Ndc10 is a platform for inner kinetochore assembly in budding yeast. Nat Struct Mol Biol 19, 48–55 (2012). https://doi.org/10.1038/nsmb.2178

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