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Architecture of the CBF3–centromere complex of the budding yeast kinetochore

Nature Structural & Molecular Biology volume 25, pages 1103–1110 (2018)Cite this article

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Abstract

Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into three centromeric determining elements (CDEs), and are associated with the centromere-specific nucleosome Cse4. Deposition of Cse4 at CEN loci is dependent on the CBF3 complex that engages CDEIII to direct Cse4 nucleosomes to CDEII. To understand how CBF3 recognizes CDEIII and positions Cse4, we determined a cryo-EM structure of a CBF3−CEN complex. CBF3 interacts with CEN DNA as a head-to-head dimer that includes the whole of CDEIII and immediate 3' regions. Specific CEN-binding of CBF3 is mediated by a Cep3 subunit of one of the CBF3 protomers that forms major groove interactions with the conserved and essential CCG and TGT motifs of CDEIII. We propose a model for a CBF3−Cse4−CEN complex with implications for understanding CBF3-directed deposition of the Cse4 nucleosome at CEN loci.

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Fig. 1: Overall structure of the dimeric CBF3−CEN3 complex.
Fig. 2: CBF3 inter-subunit interfaces.
Fig. 3: Basis for CBF3−CEN3 recognition.
Fig. 4: Model of CBF3−Cse4 nucleosome complex.

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Data availability

EM maps have been deposited with EMDB (EMD-0095, EMD-0096, EMB-0097). Protein coordinates have been deposited with RCSB (6GYP, 6GYS, 6GYU). Other data are available upon reasonable request.

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Acknowledgements

This work was funded by a MRC grant (no. MC_UP_1201/6) and a CR-UK grant (no. C576/A14109) to D.B. We thank S. Chen, G. Cannone and G. McMullan for help with EM data collection, J. Grimmett and T. Darling for computing and J. Shi for help with insect cell expression.

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  1. These authors contributed equally: Kaige Yan, Ziguo Zhang.

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  1. MRC Laboratory of Molecular Biology, Cambridge, UK

    Kaige Yan, Ziguo Zhang, Jing Yang, Stephen H. McLaughlin & David Barford

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Contributions

D.B. directed the project. Z.Z. cloned all constructs. J.Y and Z.Z. purified complexes. Z.Z. performed the mitotic stability assay. J.Y. and S.M. performed SEC-MALS experiments. K.Y. prepared EM grids, collected and analyzed EM data. K.Y. and D.B. wrote the manuscript.

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Correspondence to David Barford.

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Supplementary Figure 1 Biochemical characterization of CBF3−CEN3 complexes.

a, Left, Coomassie blue–stained SDS–PAGE of CBF3−CEN3 complex. Right, ethidium bromide staining of the same gel. Below, SEC chromatogram of (i) CBF3−CEN3, (ii) CEN3 and (iii) CBF3. b, Left, Coomassie blue–stained SDS–PAGE of CBF3core−Ndc10DBD−CEN3 complex. Right, ethidium bromide staining of the same gel. Below, SEC chromatogram of (i) CBF3core−Ndc10DBD−CEN3, (ii) CEN3 and (iii) CBF3core−Ndc10DBD. c, Mutations of I76 and Y79 of Ctf13 disrupt interactions between CBF3core and Ndc10. The experiments shown were performed in triplicate with similar results.

Supplementary Figure 2 Cryo-EM analysis and resolution of CBF3−CEN3 complex.

a, A typical cryo-EM micrograph of CBF3–CEN3 representative of 3,537 micrographs. b, Gallery of 2D class averages of CBF3−CEN3 complex showing different views representative of 100 2D classes. c, Angular distribution plot of CBF3−CEN3 particles. d, Workflow of 3D classification of CBF3−CEN3 showing a 4.4-Å map of dimeric CBF3−CEN3 complex and a 3.0-Å map of CBF3core−Ndc10DBD (lower right) (masked EM density). Red boxes, dimeric CBF3−CEN3; black box, CBF3core; blue box, monomeric CBF3−CEN3 (CBF3core and Ndc10 dimer); black box, CBF3core. The dashed-line red box shows different DNA conformations. A HEAT map representing the structural variation of the three 3D classes of the dimeric CBF3–CEN3 complex is shown in Supplementary Fig. 4c. e, Local-resolution map of multi-body segment CBF3core of CBF3A. f, Local-resolution map of multi-body segment CBF3core of CBF3B. g, Local-resolution map of multi-body segment of Ndc10DBD−CEN3−DNA. h, Cryo-EM density of the 4.4-Å CBF3−CEN3 complex (left) and local-resolution map calculated with RESMAP 56 (right). i, Fourier shell correlation (FSC) curves are shown for the cryo-EM reconstructions of CBF3–CEN3 and three multi-body segments CBF3core-A, CBF3core-B and Ndc10DBD−CEN3−DNA. j, Fourier shell correlation (FSC) curves are shown for CBF3msk (gold-standard FSC, two half maps, and merged map). The resolution at FSC = 0.5 for the model–map comparison is indicated. k, Representative EM densities of regions of the 3.0-Å map of CBF3msk.

Supplementary Figure 3 Cryo-EM analysis and resolution of CBF3core−Ndc10DBD−CEN3 complex.

a, A typical cryo-EM micrograph of CBF3core−Ndc10DBD−CEN3 complex representative of 1,171 micrographs. b, A typical cryo-EM micrograph of CBF3core–Ndc10DBD representative of 724 micrographs. These two datasets were combined for subsequent processing steps to determine 3D reconstructions of DNA-free CBF3core and CBF3core–Ndc10DBD at 3.9 Å and 3.6 Å, respectively. c, Gallery of 2D class averages of CBF3core–Ndc10DBD showing different views representative of 100 2D classes. d, Angular distribution plot of CBF3core–Ndc10DBD particles. e, Workflow of 3D classification of combined datasets from CBF3core–Ndc10DBD and CBF3core–Ndc10DBD–CEN3. Orange boxes, DNA-free CBF3core–Ndc10DBD; black boxes, CBF3core; green box, CBF3core–Ndc10DBD–CEN3 DNA complex; red boxes, dimeric CBF3core–Ndc10DBD–CEN3 complex; blue box, monomeric CBF3core–Ndc10DBD–CEN3 complex. A HEAT map representing the structural variation of the three 3D classes of DNA-free CBF3core–Ndc10DBD is shown in Supplementary Fig 4b. f, Cryo-EM density of the 3.6-Å CBF3core–Ndc10DBD complex (no DNA) (left) and local-resolution map calculated with RESMAP56 (right). g, Fourier shell correlation (FSC) curves are shown for the cryo-EM reconstructions CBF3core–Ndc10DBD and CBF3core.

Supplementary Figure 4 Structural variations of CBF3 complexes.

a, Overall structure of CBF3. b, Heat map of the r.m.s. deviation between the 3D classes DNA-free CBF3core–Ndc10DBD. Coordinates were superimposed on CBF3A. The DNA-binding module of Ndc10DBD is the most structurally variable. c, Two orthogonal views showing a HEAT map of the r.m.s. deviation between the 3D classes of the dimeric CBF3–CEN3 DNA complex.

Supplementary Figure 5 Mitotic stability assay of wild-type and mutant Ctf13.

a, Agar plate culture of yeast strains: wild type and mutants in Ctf13, the CCG motif (to AGC) of the CEN3 CDEIII or a combination of Ctf13 and CEN3 mutations. Cultures were incubated for strains harboring mini-chromosome (WT or CEN3 CDEIII CCG mutation) in combination with CTF13 (WT or I76/Y79 mutation) and grown 48 h for about 20 generations of nonselective growth for mini-chromosome. Single colonies were generated on nonselective media and further streaked onto selective media. The percentage of grown colonies on selective media was determined for mitotic transmission of mini-chromosomes. b, Table showing the percentage of colony growth on selective media (% mean survival ± 1 s.d.). Differences in mitotic stability between pairs of strains were analyzed using paired t tests. There was no significant difference between the CTF13I76R/Y79R and CEN3-CDEIIICCG/AGC mutants. The data are based on five replicates.

Supplementary Figure 6 The Cep3 subunits differ in conformation in the CBF3−CEN3 complex and schematic of the modeled CBF3−Cse4−CEN3 complex.

a, EM density map from the CBF3–CEN3 DNA complex showing the visible C termini of the two Ndc10 subunits of the Ndc10DBD dimer in close proximity. b, Superimposition of Cep3A and Cep3B of CBF3A from the CBF3–CEN3 DNA complex. CEN3 DNA as bound to Cep3A of CBF3A is shown. The Zn2Cys6 cluster and αMN helix of Cep3A interact with the major grooves of the CCG and TGT motifs of CDEIII, respectively. The major differences between Cep3A and Cep3B involve these structural elements. c, Schematic of Fig. 4b showing the modeled CBF3–Cse4–CEN3 complex. The Cse4 nucleosome is depicted with left-handed chirality. d, Cse4 nucleosome with right-handed chirality. In this instance, the Cse4 nucleosome clashes with CBF3A and therefore represents a less likely scenario. CBF3 is shown transparent.

Supplementary Figure 7 SEC-MALS analysis of CBF3−CEN3 complexes.

a, SEC MALS chromatogram for CBF3 complex without CEN3–DNA shows two species of molecular mass 888 kDa and 454 kDa, corresponding to dimeric CBF3 ([Cep3]2–Ctf13–Skp1–[Ndc10]2)2 (expected mass of 453 kDa) and monomeric CBF3 ([Cep3]2–Ctf13–Skp1–[Ndc10]2) (expected mass of 906 kDa). b, In the presence of CEN3 DNA, all CBF3 migrates as a single species of molecular mass 1,018 kDa corresponding to a dimeric CBF3–CEN3 complex ([Cep3]2–Ctf13–Skp1–[Ndc10]2)2–CEN3 (expected mass of 1,010 kDa). The experiments shown were performed in triplicate with similar results.

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Supplementary Figures 1–7 and Supplementary Table 1

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Supplementary Video 1

Cryo-EM structure of CBF3–CEN3. Video to show the dimeric structure of CBF3 in complex with CEN3 DNA. Shown is the EM density map of the complex with a transparent surface, with the subunits of CBF3 and CEN3 DNA as cartoon representations. Based on EM map EMD-0096 and PDB code 6GYS.

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Yan, K., Zhang, Z., Yang, J. et al. Architecture of the CBF3–centromere complex of the budding yeast kinetochore. Nat Struct Mol Biol 25, 1103–1110 (2018). https://doi.org/10.1038/s41594-018-0154-1

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