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Cited by 42Microtubule and mitosis dynamicsGenomics and Chromatin DynamicsDNA Repair Mechanisms

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Structure of the human outer kinetochore KMN network complex

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Yatskevich, Stanislau, Yang, Jing, Bellini, Dom, Zhang, Ziguo, Barford, David·2024·Nature Structural & Molecular Biology
DOI 10.1038/s41594-024-01249-yPMC PMC11189301

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Abstract

Faithful chromosome segregation requires robust, load-bearing attachments of chromosomes to the mitotic spindle, a function accomplished by large macromolecular complexes termed kinetochores. In most eukaryotes, the constitutive centromere-associated network (CCAN) complex of the inner kinetochore recruits to centromeres the ten-subunit outer kinetochore KMN network that comprises the KNL1C, MIS12C and NDC80C complexes. The KMN network directly attaches CCAN to microtubules through MIS12C and NDC80C. Here, we determined a high-resolution cryo-EM structure of the human KMN network. This showed an intricate and extensive assembly of KMN subunits, with the central MIS12C forming rigid interfaces with NDC80C and KNL1C, augmented by multiple peptidic inter-subunit connections. We also observed that unphosphorylated MIS12C exists in an auto-inhibited state that suppresses its capacity to interact with CCAN. Ser100 and Ser109 of the N-terminal segment of the MIS12C subunit Dsn1, two key targets of Aurora B kinase, directly stabilize this auto-inhibition. Our study indicates how selectively relieving this auto-inhibition through Ser100 and Ser109 phosphorylation might restrict outer kinetochore assembly to functional centromeres during cell division.

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Research works printed but not linked: 52

  1. McAinsh, A. D. & Marston, A. L. The four causes: the functional architecture of centromeres and kinetochores. Annu. Rev. Genet. 56, 279–314 (2022). · DOI
  2. Yatskevich, S., Barford, D. & Muir, K. W. Conserved and divergent mechanisms of inner kinetochore assembly onto centromeric chromatin. Curr. Opin. Struct. Biol. 81, 102638 (2023). · DOI
  3. Musacchio, A. & Desai, A. A molecular view of kinetochore assembly and function. Biology 6, 5 (2017). · DOI
  4. Navarro, A. P. & Cheeseman, I. M. Kinetochore assembly throughout the cell cycle. Semin. Cell Dev. Biol. 117, 62–74 (2021). · DOI
  5. Fischer, E. S. Kinetochore-catalyzed MCC formation: A structural perspective. IUBMB Life 75, 289–310 (2023). · DOI
  6. McAinsh, A. D. & Kops, G. Principles and dynamics of spindle assembly checkpoint signalling. Nat. Rev. Mol. Cell Biol. 24, 543–559 (2023). · DOI
  7. Lara-Gonzalez, P., Pines, J. & Desai, A. Spindle assembly checkpoint activation and silencing at kinetochores. Semin. Cell Dev. Biol. 117, 86–98 (2021). · DOI
  8. van Hooff, J. J., Tromer, E., van Wijk, L. M., Snel, B. & Kops, G. J. Evolutionary dynamics of the kinetochore network in eukaryotes as revealed by comparative genomics. EMBO Rep. 18, 1559–1571 (2017). · DOI
  9. Dimitrova, Y. N., Jenni, S., Valverde, R., Khin, Y. & Harrison, S. C. Structure of the MIND complex defines a regulatory focus for yeast kinetochore assembly. Cell. 167, 1014–1027 (2016). · DOI
  10. Petrovic, A. et al. Structure of the MIS12 complex and molecular basis of its interaction with CENP-C at human kinetochores. Cell 167, 1028–1040 (2016). · DOI
  11. Petrovic, A. et al. Modular assembly of RWD domains on the Mis12 complex underlies outer kinetochore organization. Mol Cell 53, 591–605 (2014). · DOI
  12. Petrovic, A. et al. The MIS12 complex is a protein interaction hub for outer kinetochore assembly. J. Cell Biol. 190, 835–852 (2010). · DOI
  13. Screpanti, E. et al. Direct binding of Cenp-C to the Mis12 complex joins the inner and outer kinetochore. Curr. Biol. 21, 391–398 (2011). · DOI
  14. Hara, M., Ariyoshi, M., Okumura, E. I., Hori, T. & Fukagawa, T. Multiple phosphorylations control recruitment of the KMN network onto kinetochores. Nat. Cell Biol. 20, 1378–1388 (2018). · DOI
  15. Gascoigne, K. E. et al. Induced ectopic kinetochore assembly bypasses the requirement for CENP-A nucleosomes. Cell 145, 410–422 (2011). · DOI
  16. Rago, F., Gascoigne, K. E. & Cheeseman, I. M. Distinct organization and regulation of the outer kinetochore KMN network downstream of CENP-C and CENP-T. Curr. Biol. 25, 671–677 (2015). · DOI
  17. Huis In ‘t Veld, P. J. et al. Molecular basis of outer kinetochore assembly on CENP-T. eLife 5, e21007 (2016). · DOI
  18. Walstein, K. et al. Assembly principles and stoichiometry of a complete human kinetochore module. Sci. Adv. 7, eabg1037 (2021). · DOI
  19. Przewloka, M. R. et al. CENP-C is a structural platform for kinetochore assembly. Curr. Biol. 21, 399–405 (2011). · DOI
  20. Powers, A. F. et al. The Ndc80 kinetochore complex forms load-bearing attachments to dynamic microtubule tips via biased diffusion. Cell 136, 865–875 (2009). · DOI
  21. Ciferri, C. et al. Implications for kinetochore–microtubule attachment from the structure of an engineered Ndc80 complex. Cell 133, 427–439 (2008). · DOI
  22. DeLuca, J. G. et al. Kinetochore microtubule dynamics and attachment stability are regulated by Hec1. Cell 127, 969–982 (2006). · DOI
  23. Valverde, R., Ingram, J. & Harrison, S. C. Conserved tetramer junction in the kinetochore Ndc80 complex. Cell Rep. 17, 1915–1922 (2016). · DOI
  24. Alushin, G. M. et al. The Ndc80 kinetochore complex forms oligomeric arrays along microtubules. Nature 467, 805–810 (2010). · DOI
  25. McIntosh, J. R. et al. Fibrils connect microtubule tips with kinetochores: a mechanism to couple tubulin dynamics to chromosome motion. Cell 135, 322–333 (2008). · DOI
  26. Maure, J. F. et al. The Ndc80 loop region facilitates formation of kinetochore attachment to the dynamic microtubule plus end. Curr. Biol. 21, 207–213 (2011). · DOI
  27. Polley, S. et al. Stable kinetochore–microtubule attachment requires loop-dependent Ndc80–Ndc80 binding. EMBO J. 42, e112504 (2023). · DOI · Paper page
  28. Malvezzi, F. et al. A structural basis for kinetochore recruitment of the Ndc80 complex via two distinct centromere receptors. EMBO J. 32, 409–423 (2013). · DOI
  29. Nishino, T. et al. CENP-T provides a structural platform for outer kinetochore assembly. EMBO J. 32, 424–436 (2013). · DOI
  30. Kiyomitsu, T., Murakami, H. & Yanagida, M. Protein interaction domain mapping of human kinetochore protein Blinkin reveals a consensus motif for binding of spindle assembly checkpoint proteins Bub1 and BubR1. Mol. Cell. Biol. 31, 998–1011 (2011). · DOI
  31. Raisch, T. et al. Structure of the RZZ complex and molecular basis of Spindly-driven corona assembly at human kinetochores. EMBO J. 41, e110411 (2022). · DOI
  32. Welburn, J. P. et al. Aurora B phosphorylates spatially distinct targets to differentially regulate the kinetochore-microtubule interface. Mol. Cell 38, 383–392 (2010). · DOI
  33. Roscioli, E. et al. Ensemble-level organization of human kinetochores and evidence for distinct tension and attachment sensors. Cell Rep. 31, 107535 (2020). · DOI
  34. Emanuele, M. J. et al. Aurora B kinase and protein phosphatase 1 have opposing roles in modulating kinetochore assembly. J. Cell Biol. 181, 241–254 (2008). · DOI
  35. Kim, S. & Yu, H. Multiple assembly mechanisms anchor the KMN spindle checkpoint platform at human mitotic kinetochores. J. Cell Biol. 208, 181–196 (2015). · DOI
  36. Yang, Y. et al. Phosphorylation of HsMis13 by Aurora B kinase is essential for assembly of functional kinetochore. J. Biol. Chem. 283, 26726–26736 (2008). · DOI
  37. Akiyoshi, B., Nelson, C. R. & Biggins, S. The aurora B kinase promotes inner and outer kinetochore interactions in budding yeast. Genetics 194, 785–789 (2013). · DOI
  38. Takenoshita, Y., Hara, M. & Fukagawa, T. Recruitment of two Ndc80 complexes via the CENP-T pathway is sufficient for kinetochore functions. Nat. Commun. 13, 851 (2022). · DOI
  39. Polley, S. et al. Insights into human outer kinetochore assembly and force transmission from a structure-function analysis of the KMN network. Nat. Struct. Mol. Biol. (2023). · DOI
  40. Scarborough, E. A., Davis, T. N. & Asbury, C. L. Tight bending of the Ndc80 complex provides intrinsic regulation of its binding to microtubules. eLife 8, e44489 (2019). · DOI
  41. Wan, X. et al. Protein architecture of the human kinetochore microtubule attachment site. Cell 137, 672–684 (2009). · DOI
  42. Liu, D., Vader, G., Vromans, M. J., Lampson, M. A. & Lens, S. M. Sensing chromosome bi-orientation by spatial separation of aurora B kinase from kinetochore substrates. Science 323, 1350–1353 (2009). · DOI
  43. Zhang, Z., Yang, J. & Barford, D. Recombinant expression and reconstitution of multiprotein complexes by the USER cloning method in the insect cell-baculovirus expression system. Methods 95, 13–25 (2016). · DOI
  44. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017). · DOI
  45. Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015). · DOI
  46. Zivanov, J. et al. A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0. eLife. 11, e83724 (2022). · DOI
  47. Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019). · DOI
  48. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017). · DOI · Paper page
  49. Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021). · DOI
  50. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010). · DOI · Paper page
  51. Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58, 1948–1954 (2002). · DOI · Paper page
  52. Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M. & Barton, G. J. Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009). · DOI

Metadata

Authors
Yatskevich, S., Yang, J., Bellini, D., Zhang, Z., & Barford, D.
Affiliations
MRC Laboratory of Molecular Biology (GB)
Corresponding author
  • Yatskevich, Stanislau
  • Barford, David
ORCID
Venue
Nature Structural & Molecular Biology
Publisher
Springer Science and Business Media LLC
Published
2024-03-08
Volume
31
Issue
6
Pages
874-883
ISSN
  • 1545-9985 (ISSN-L)
  • 1545-9993
DOI
10.1038/s41594-024-01249-y
PMC
PMC11189301
OpenAlex
W4392582038
Cited by
42
References
1
Citations by year
2026: 14 · 2025: 15 · 2024: 12
FWCI
9.17
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Structural & Molecular Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Apollo (University of Cambridge) (acceptedVersion, cc-by)
Funders
  • UK Research and Innovation (MC_UP_1201/6)
  • Cancer Research UK
  • Medical Research Council (MC_UP_1201/6, MR/X012182/1)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Keywords
outer kinetochore, KMN network, Mis12 complex, Ndc80 complex, chromosome segregation, autoinhibition, DSN1, centromere, protein complex structure
MeSH terms
Chromosomal Proteins, Non-Histone, Cytoskeletal Proteins, Humans, Microtubule-Associated Proteins, Models, Molecular, Nuclear Proteins, Phosphorylation, Protein Conformation, Kinetochores, Cell Cycle Proteins, Cryoelectron Microscopy, Aurora Kinase B

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