Implications for kinetochore-microtubule attachment from the structure of an engineered Ndc80 complex

Abstract

Kinetochores are proteinaceous assemblies that mediate the interaction of chromosomes with the mitotic spindle. The 180 kDa Ndc80 complex is a direct point of contact between kinetochores and microtubules. Its four subunits contain coiled coils and form an elongated rod structure with functional globular domains at either end. We crystallized an engineered "bonsai" Ndc80 complex containing a shortened rod domain but retaining the globular domains required for kinetochore localization and microtubule binding. The structure reveals a microtubule-binding interface containing a pair of tightly interacting calponin-homology (CH) domains with a previously unknown arrangement. The interaction with microtubules is cooperative and predominantly electrostatic. It involves positive charges in the CH domains and in the N-terminal tail of the Ndc80 subunit and negative charges in tubulin C-terminal tails and is regulated by the Aurora B kinase. We discuss our results with reference to current models of kinetochore-microtubule attachment and centromere organization.

Figure 1. Properties of Ndc80^bonsai

(A) Organization of Ndc80 subunits. (B) Scheme of Ndc80-Spc25 and Nuf2-Spc24 fusion proteins. Residues 1–286 of Ndc80 (Ndc80^1–286) were fused to residues 118–224 of Spc25 (Spc25^118–224). Residues 1–169 of Nuf2 (Nuf2^1–169) were fused to residues 122–197 of Spc24 (Spc24^122–197). Red circles with “P” mark phosphorylation sites in the Ndc80 N-terminal tail (Cheeseman et al., 2006; DeLuca et al., 2006; Wei et al., 2007). (C) Ndc80-Spc25 and Nuf2-Spc24 fusions were coexpressed in E. coli and purified to homogeneity. (D) When injected in HeLa cells, Alexa Fluor 488-labeled Ndc80^bonsai stained kinetochores throughout mitosis. (E) Partition of the Ndc80^bonsai complex in pellet (P) and supernatant (S) fractions in cosedimentation assay with increasing concentrations of polymeric tubulin. (F) Negative stain EM images of Paclitaxel-stabilized microtubules in the absence (left) and presence (right) of bound Ndc80^bonsai. A thick halo of protein surrounds the microtubules bound by Ndc80^bonsai, giving them a hairy appearance. Insets are 2.5×. Bar = 100 nm.

Figure 2. Crystal Structure of Ndc80^DN-bonsai

(A) Ribbon model of Ndc80^ΔN-bonsai. The structure is colored as in Figure 1A. (B) Sequence of the Ndc80-Spc25 fusion protein. Numbering refers to human sequences. Residues are colored based on level of conservation. Circles under residues indicate a contact, and the color of the circle is the color of the contacted subunit (for instance, yellow = Nuf2). Residues are in contact when they form hydrogen bonds or salt bridges, or when they are less than 4 Å away, or when they bury more than 40% of the solvent-accessible surface in the interaction, calculated with PISA (Krissinel and Henrick, 2007). (C) Sequence of the Nuf2-Spc24 fusion analyzed as in (B).

Figure 3. Organization of the CH Domains in the Ndc80-Nuf2 Subcomplex

(A) Topology diagram of Ndc80 and Nuf2. The CH domain is contained between the αA and αG helices. (B) Two views of the superposition of the CH domains of Ndc80 and Nuf2. Note the conspicuous bending of the tips of the Nuf2 αE helix. (C) Structure-based sequence alignment of the CH domains of Ndc80, Nuf2, and EB1. The αA, αC, αE, and αG helices are contoured. Residues highlighted in gray have their side chains buried in the hydrophobic core of the CH domain. (D) General view and closeups of the interface of Ndc80 and Nuf2.

Figure 4. Organization of the Microtubule-Binding Region

(A) Surface views of the Ndc80-Nuf2 globular region colored according to conservation. (B) Surface views colored by electrostatic potential. The orientations are as in (A). (C) Positions of mutated residues. Residues whose KE mutation caused a 30- to 40-fold impairment of microtubule binding are shown in purple (see also panel D, Table S1, and Figure S2). Residues whose KE mutation caused a 6- to 12-fold impairment in microtubule binding are shown in magenta. Residues whose mutation into alanine provided modest destabilization of binding that was not quantitated are shown in pink. (D) Plot of quantifications of microtubule cosedimentation assay with Ndc80^bonsai and the indicated mutants (see also Table S1 and Figure S2). Error bars represent standard deviations calculated from at least three independent experiments. (E) The ability of Ndc80^bonsai and Ndc80^ΔN-bonsai to cosediment with microtubules was tested in parallel. (F) Ndc80^bonsai showed strongly reduced binding to subtilisin-treated microtubules (see Supplemental Experimental Procedures for details). (G) Aurora B releases Ndc80^bonsai from microtubules. (H) Sequence of the N-terminal tail of Ndc80. Residues in red were phosphorylated by Aurora B in vitro (see Supplemental Experimental Procedures). Residues in green are phosphorylated in vivo but do not conform to the Aurora B consensus. Ser4 (blue) could not be assigned unambiguously.

Figure 5. Visualization of Microtubule Binding

(A) A mix of rhodamine-labeled tubulin:tubulin at a 0.16 ratio and final concentration of 100 nM was polymerized and incubated with increasing amounts of Alexa-Ndc80^bonsai. N/T is the Ndc80^bonsai/tubulin concentration ratio. (B) Inset from N/T = 0.125 showing clusters of fluorescent Ndc80^bonsai on microtubules. (C) Line scans of two representative microtubules. The net fluorescence intensity (signal – background) at each pixel was divided by the mean net fluorescence intensity along the line scan. (D) Inset from N/T = 4.0 showing even distribution of Ndc80^bonsai. (E) Line scans of two representative microtubule analyses as for (C).

Figure 6. Models of Ndc80 and Microtubule- Kinetochore Interaction

(A–D) Models of the Ndc80-microtubule interaction. A yellow patch on tubulin in (A) and (B) represents a hypothetical binding site for the Ndc80 N-terminal tail. In (C), it is hypothesized that the N-terminal tail binds to the negatively charged patch on Nuf2, shown in Figure 4B. (E) The Ndc80^bonsai complex. (F) Summary of crosslinking analysis (Maiolica et al., 2007). Connected black dots mark crosslinked residues. Numbers in hexagons define distances between “milestones,” such as subsequent crosslinked residues or pairs of interacting residues identified in the structure. (G) Model of the full-length Ndc80 complex showing the predicted break in the coiled-coil region. (H) Implications from the structure of the Ndc80 complex on the organization of the microtubule-kinetochore interface.