Structure of the Ndc80 complex and its interactions at the yeast kinetochore–microtubule interface

Zahm, Jacob A.; Jenni, Simon; Harrison, Stephen C.

doi:10.1098/rsob.220378

Structure of the Ndc80 complex and its interactions at the yeast kinetochore–microtubule interface

Journal Article · Wed Mar 08 00:00:00 EST 2023 · Open Biology

DOI:https://doi.org/10.1098/rsob.220378· OSTI ID:2469543

^[1]; ^[1]; ^[2]

Harvard University, Boston, MA (United States)
Harvard University, Boston, MA (United States); Harvard Medical School, Boston, MA (United States)

The conserved Ndc80 kinetochore complex, Ndc80c, is the principal link between mitotic spindle microtubules and centromere-associated proteins. We used AlphaFold 2 (AF2) to obtain predictions of the Ndc80 ‘loop’ structure and of the Ndc80 : Nuf2 globular head domains that interact with the Dam1 subunit of the heterodecameric DASH/Dam1 complex (Dam1c). The predictions guided design of crystallizable constructs, with structures close to the predicted ones. The Ndc80 ‘loop’ is a stiff, α-helical ‘switchback’ structure; AF2 predictions and positions of preferential cleavage sites indicate that flexibility within the long Ndc80c rod occurs instead at a hinge closer to the globular head. Conserved stretches of the Dam1 C terminus bind Ndc80c such that phosphorylation of Dam1 serine residues 257, 265 and 292 by the mitotic kinase Ipl1/Aurora B can release this contact during error correction of mis-attached kinetochores. We integrate the structural results presented here into our current molecular model of the kinetochore–microtubule interface. The model illustrates how multiple interactions between Ndc80c, DASH/Dam1c and the microtubule lattice stabilize kinetochore attachments.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: American Cancer Society; National Institutes of Health (NIH); USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 2469543

Journal Information:: Open Biology, Journal Name: Open Biology Journal Issue: 3 Vol. 13; ISSN 2046-2441

Publisher:: The Royal SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (69)

Phospho-Regulation of Kinetochore-Microtubule Attachments by the Aurora Kinase Ipl1p Cheeseman, Iain M.; Anderson, Scott; Jwa, Miri Cell, Vol. 111, Issue 2 https://doi.org/10.1016/S0092-8674(02)00973-X	journal	October 2002
Implications for Kinetochore-Microtubule Attachment from the Structure of an Engineered Ndc80 Complex Ciferri, Claudio; Pasqualato, Sebastiano; Screpanti, Emanuela Cell, Vol. 133, Issue 3 https://doi.org/10.1016/j.cell.2008.03.020	journal	May 2008
A TOG Protein Confers Tension Sensitivity to Kinetochore-Microtubule Attachments Miller, Matthew P.; Asbury, Charles L.; Biggins, Sue Cell, Vol. 165, Issue 6 https://doi.org/10.1016/j.cell.2016.04.030	journal	June 2016
Structure of the MIND Complex Defines a Regulatory Focus for Yeast Kinetochore Assembly Dimitrova, Yoana N.; Jenni, Simon; Valverde, Roberto Cell, Vol. 167, Issue 4 https://doi.org/10.1016/j.cell.2016.10.011	journal	November 2016
Conserved Tetramer Junction in the Kinetochore Ndc80 Complex Valverde, Roberto; Ingram, Jessica; Harrison, Stephen C. Cell Reports, Vol. 17, Issue 8 https://doi.org/10.1016/j.celrep.2016.10.065	journal	November 2016
Mps1 Phosphorylation of Dam1 Couples Kinetochores to Microtubule Plus Ends at Metaphase Shimogawa, Michelle M.; Graczyk, Beth; Gardner, Melissa K. Current Biology, Vol. 16, Issue 15 https://doi.org/10.1016/j.cub.2006.06.063	journal	August 2006
Ndc80 Internal Loop Interacts with Dis1/TOG to Ensure Proper Kinetochore-Spindle Attachment in Fission Yeast Hsu, Kuo-Shun; Toda, Takashi Current Biology, Vol. 21, Issue 3 https://doi.org/10.1016/j.cub.2010.12.048	journal	February 2011
The Ndc80 Loop Region Facilitates Formation of Kinetochore Attachment to the Dynamic Microtubule Plus End Maure, Jean-François; Komoto, Shinya; Oku, Yusuke Current Biology, Vol. 21, Issue 3 https://doi.org/10.1016/j.cub.2010.12.050	journal	February 2011
Lateral to End-on Conversion of Chromosome-Microtubule Attachment Requires Kinesins CENP-E and MCAK Shrestha, Roshan L.; Draviam, Viji M. Current Biology, Vol. 23, Issue 16 https://doi.org/10.1016/j.cub.2013.06.040	journal	August 2013
Cdk1 Phosphorylation of the Dam1 Complex Strengthens Kinetochore-Microtubule Attachments Gutierrez, Abraham; Kim, Jae ook; Umbreit, Neil T. Current Biology, Vol. 30, Issue 22 https://doi.org/10.1016/j.cub.2020.08.054	journal	November 2020
Architecture and Flexibility of the Yeast Ndc80 Kinetochore Complex Wang, Hong-Wei; Long, Sydney; Ciferri, Claudio Journal of Molecular Biology, Vol. 383, Issue 4 https://doi.org/10.1016/j.jmb.2008.08.077	journal	November 2008
The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes van Zundert, G. C. P.; Rodrigues, J. P. G. L. M.; Trellet, M. Journal of Molecular Biology, Vol. 428, Issue 4 https://doi.org/10.1016/j.jmb.2015.09.014	journal	February 2016
Formation of a Dynamic Kinetochore- Microtubule Interface through Assembly of the Dam1 Ring Complex Westermann, Stefan; Avila-Sakar, Agustin; Wang, Hong-Wei Molecular Cell, Vol. 17, Issue 2 https://doi.org/10.1016/j.molcel.2004.12.019	journal	January 2005
Structure of a Central Component of the Yeast Kinetochore: The Spc24p/Spc25p Globular Domain Wei, Ronnie R.; Schnell, Jason R.; Larsen, Nicholas A. Structure, Vol. 14, Issue 6 https://doi.org/10.1016/j.str.2006.04.007	journal	June 2006
CENP-T provides a structural platform for outer kinetochore assembly Nishino, Tatsuya; Rago, Florencia; Hori, Tetsuya The EMBO Journal, Vol. 32, Issue 3 https://doi.org/10.1038/emboj.2012.348	journal	January 2013
A structural basis for kinetochore recruitment of the Ndc80 complex via two distinct centromere receptors Malvezzi, Francesca; Litos, Gabriele; Schleiffer, Alexander The EMBO Journal, Vol. 32, Issue 3 https://doi.org/10.1038/emboj.2012.356	journal	January 2013
Stabilization of microtubule dynamics at anaphase onset promotes chromosome segregation Higuchi, Toru; Uhlmann, Frank Nature, Vol. 433, Issue 7022 https://doi.org/10.1038/nature03240	journal	January 2005
Molecular mechanisms of kinetochore capture by spindle microtubules Tanaka, Kozo; Mukae, Naomi; Dewar, Hilary Nature, Vol. 434, Issue 7036 https://doi.org/10.1038/nature03483	journal	April 2005
The Ndc80 kinetochore complex forms oligomeric arrays along microtubules Alushin, Gregory M.; Ramey, Vincent H.; Pasqualato, Sebastiano Nature, Vol. 467, Issue 7317 https://doi.org/10.1038/nature09423	journal	October 2010
Kinetochores require oligomerization of Dam1 complex to maintain microtubule attachments against tension and promote biorientation Umbreit, Neil T.; Miller, Matthew P.; Tien, Jerry F. Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms5951	journal	September 2014
A quantitative description of Ndc80 complex linkage to human kinetochores Suzuki, Aussie; Badger, Benjamin L.; Salmon, Edward D. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9161	journal	September 2015
The Ndc80/HEC1 complex is a contact point for kinetochore-microtubule attachment Wei, Ronnie R.; Al-Bassam, Jawdat; Harrison, Stephen C. Nature Structural & Molecular Biology, Vol. 14, Issue 1 https://doi.org/10.1038/nsmb1186	journal	December 2006
The yeast DASH complex forms closed rings on microtubules Miranda, Jj L.; Wulf, Peter De; Sorger, Peter K. Nature Structural & Molecular Biology, Vol. 12, Issue 2 https://doi.org/10.1038/nsmb896	journal	January 2005
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
The phosphorylation of a kinetochore protein Dam1 by Aurora B/Ipl1 kinase promotes chromosome bipolar attachment in yeast Jin, Fengzhi; Bokros, Michael; Wang, Yanchang Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-12329-z	journal	September 2017
Microtubule depolymerization can drive poleward chromosome motion in fission yeast Grishchuk, Ekaterina L.; McIntosh, J. Richard The EMBO Journal, Vol. 25, Issue 20 https://doi.org/10.1038/sj.emboj.7601353	journal	October 2006
Molecular organization of the Ndc80 complex, an essential kinetochore component Wei, R. R.; Sorger, P. K.; Harrison, S. C. Proceedings of the National Academy of Sciences, Vol. 102, Issue 15 https://doi.org/10.1073/pnas.0501168102	journal	April 2005
Phosphoregulation promotes release of kinetochores from dynamic microtubules via multiple mechanisms Sarangapani, K. K.; Akiyoshi, B.; Duggan, N. M. Proceedings of the National Academy of Sciences, Vol. 110, Issue 18 https://doi.org/10.1073/pnas.1220700110	journal	April 2013
Architecture of the Human Ndc80-Hec1 Complex, a Critical Constituent of the Outer Kinetochore Ciferri, Claudio; De Luca, Jennifer; Monzani, Silvia Journal of Biological Chemistry, Vol. 280, Issue 32 https://doi.org/10.1074/jbc.M504070200	journal	June 2005
Structural Analysis of Multiprotein Complexes by Cross-linking, Mass Spectrometry, and Database Searching Maiolica, Alessio; Cittaro, Davide; Borsotti, Dario Molecular & Cellular Proteomics, Vol. 6, Issue 12 https://doi.org/10.1074/mcp.M700274-MCP200	journal	October 2007
Mitotic Spindle Integrity and Kinetochore Function Linked by the Duo1p/Dam1p Complex Cheeseman, Iain M.; Enquist-Newman, Maria; Müller-Reichert, Thomas The Journal of Cell Biology, Vol. 152, Issue 1 https://doi.org/10.1083/jcb.152.1.197	journal	January 2001
Molecular mechanisms of microtubule-dependent kinetochore transport toward spindle poles Tanaka, Kozo; Kitamura, Etsushi; Kitamura, Yoko The Journal of Cell Biology, Vol. 178, Issue 2 https://doi.org/10.1083/jcb.200702141	journal	July 2007
Cooperation of the Dam1 and Ndc80 kinetochore complexes enhances microtubule coupling and is regulated by aurora B Tien, Jerry F.; Umbreit, Neil T.; Gestaut, Daniel R. The Journal of Cell Biology, Vol. 189, Issue 4 https://doi.org/10.1083/jcb.200910142	journal	May 2010
The Dam1 complex confers microtubule plus end–tracking activity to the Ndc80 kinetochore complex Lampert, Fabienne; Hornung, Peter; Westermann, Stefan The Journal of Cell Biology, Vol. 189, Issue 4 https://doi.org/10.1083/jcb.200912021	journal	May 2010
Conserved and divergent features of kinetochores and spindle microtubule ends from five species McIntosh, J. Richard; O’Toole, Eileen; Zhudenkov, Kirill The Journal of Cell Biology, Vol. 200, Issue 4 https://doi.org/10.1083/jcb.201209154	journal	February 2013
Molecular requirements for the formation of a kinetochore–microtubule interface by Dam1 and Ndc80 complexes Lampert, Fabienne; Mieck, Christine; Alushin, Gregory M. The Journal of Cell Biology, Vol. 200, Issue 1 https://doi.org/10.1083/jcb.201210091	journal	December 2012
Structural differences between yeast and mammalian microtubules revealed by cryo-EM Howes, Stuart C.; Geyer, Elisabeth A.; LaFrance, Benjamin Journal of Cell Biology, Vol. 216, Issue 9 https://doi.org/10.1083/jcb.201612195	journal	June 2017
Three interacting regions of the Ndc80 and Dam1 complexes support microtubule tip-coupling under load Flores, Rachel L.; Peterson, Zachary E.; Zelter, Alex Journal of Cell Biology, Vol. 221, Issue 5 https://doi.org/10.1083/jcb.202107016	journal	March 2022
Electron tomography reveals aspects of spindle structure important for mechanical stability at metaphase O’Toole, Eileen; Morphew, Mary; McIntosh, J. Richard Molecular Biology of the Cell, Vol. 31, Issue 3 https://doi.org/10.1091/mbc.E19-07-0405	journal	February 2020
Protein Arms in the Kinetochore-Microtubule Interface of the Yeast DASH Complex Miranda, Jj L.; King, David S.; Harrison, Stephen C. Molecular Biology of the Cell, Vol. 18, Issue 7 https://doi.org/10.1091/mbc.e07-02-0135	journal	July 2007
The Dam1 ring binds to the E-hook of tubulin and diffuses along the microtubule Ramey, Vincent H.; Wang, Hong-Wei; Nakajima, Yuko Molecular Biology of the Cell, Vol. 22, Issue 4 https://doi.org/10.1091/mbc.e10-10-0841	journal	February 2011
Coiled-coil networking shapes cell molecular machinery Wang, Yongqiang; Zhang, Xinlei; Zhang, Hong Molecular Biology of the Cell, Vol. 23, Issue 19 https://doi.org/10.1091/mbc.e12-05-0396	journal	October 2012
The internal loop of fission yeast Ndc80 binds Alp7/TACC-Alp14/TOG and ensures proper chromosome attachment Tang, Ngang Heok; Takada, Hirofumi; Hsu, Kuo-Shun Molecular Biology of the Cell, Vol. 24, Issue 8 https://doi.org/10.1091/mbc.e12-11-0817	journal	April 2013
Unique Phylogenetic Distributions of the Ska and Dam1 Complexes Support Functional Analogy and Suggest Multiple Parallel Displacements of Ska by Dam1 van Hooff, Jolien J. E.; Snel, Berend; Kops, Geert J. P. L. Genome Biology and Evolution, Vol. 9, Issue 5 https://doi.org/10.1093/gbe/evx088	journal	May 2017
Molecular architecture of the Dam1 complex–microtubule interaction Legal, Thibault; Zou, Juan; Sochaj, Alicja Open Biology, Vol. 6, Issue 3 https://doi.org/10.1098/rsob.150237	journal	March 2016
Kinetochore–microtubule interaction during S phase in Saccharomyces cerevisiae Kitamura, Etsushi; Tanaka, Kozo; Kitamura, Yoko Genes & Development, Vol. 21, Issue 24 https://doi.org/10.1101/gad.449407	journal	December 2007
Molecular Structures of Yeast Kinetochore Subcomplexes and Their Roles in Chromosome Segregation Jenni, Simon; Dimitrova, Yoana N.; Valverde, Roberto Cold Spring Harbor Symposia on Quantitative Biology, Vol. 82 https://doi.org/10.1101/sqb.2017.82.033738	journal	January 2017
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Improved methods for building protein models in electron density maps and the location of errors in these models Jones, T. A.; Zou, J. Y.; Cowan, S. W. Acta Crystallographica Section A Foundations of Crystallography, Vol. 47, Issue 2, p. 110-119 https://doi.org/10.1107/S0108767390010224	journal	March 1991
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion Painter, Jay; Merritt, Ethan A. Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 4 https://doi.org/10.1107/S0907444906005270	journal	March 2006
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
FEM: feature-enhanced map Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 3 https://doi.org/10.1107/S1399004714028132	journal	February 2015
Real-space refinement in PHENIX for cryo-EM and crystallography Afonine, Pavel V.; Poon, Billy K.; Read, Randy J. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6 https://doi.org/10.1107/S2059798318006551	journal	May 2018
xia2.multiplex: a multi-crystal data-analysis pipeline Gildea, Richard J.; Beilsten-Edmands, James; Axford, Danny Acta Crystallographica Section D Structural Biology, Vol. 78, Issue 6 https://doi.org/10.1107/S2059798322004399	journal	May 2022
CCP4 Cloud for structure determination and project management in macromolecular crystallography Krissinel, Eugene; Lebedev, Andrey A.; Uski, Ville Acta Crystallographica Section D Structural Biology, Vol. 78, Issue 9 https://doi.org/10.1107/S2059798322007987	journal	August 2022
Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface Jenni, Simon; Harrison, Stephen C. Science, Vol. 360, Issue 6388 https://doi.org/10.1126/science.aar6436	journal	May 2018
Ipl1-dependent phosphorylation of Dam1 is reduced by tension applied on kinetochores Keating, Patrick; Rachidi, Najma; Tanaka, Tomoyuki U. Journal of Cell Science, Vol. 122, Issue 23 https://doi.org/10.1242/jcs.055566	journal	December 2009
Kinetochore-associated Stu2 promotes chromosome biorientation in vivo Miller, Matthew P.; Evans, Rena K.; Zelter, Alex PLOS Genetics, Vol. 15, Issue 10 https://doi.org/10.1371/journal.pgen.1008423	journal	October 2019
RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design Huang, Po-Ssu; Ban, Yih-En Andrew; Richter, Florian PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0024109	journal	August 2011
Kinetochore Biorientation in Saccharomyces cerevisiae Requires a Tightly Folded Conformation of the Ndc80 Complex Tien, Jerry F.; Umbreit, Neil T.; Zelter, Alex Genetics, Vol. 198, Issue 4 https://doi.org/10.1534/genetics.114.167775	journal	September 2014
The DASH Complex Component Ask1 Is a Cell Cycle-Regulated Cdk Substrate inSaccharomyces cerevisiae Li, Yumei; Elledge, Stephen J. Cell Cycle, Vol. 2, Issue 2 https://doi.org/10.4161/cc.2.2.336	journal	March 2003
Molecular basis of outer kinetochore assembly on CENP-T Huis in 't Veld, Pim J.; Jeganathan, Sadasivam; Petrovic, Arsen eLife, Vol. 5 https://doi.org/10.7554/eLife.21007	journal	December 2016
The Ndc80 complex bridges two Dam1 complex rings Kim, Jae ook; Zelter, Alex; Umbreit, Neil T. eLife, Vol. 6 https://doi.org/10.7554/eLife.21069	journal	February 2017
chTOG is a conserved mitotic error correction factor Herman, Jacob A.; Miller, Matthew P.; Biggins, Sue eLife, Vol. 9 https://doi.org/10.7554/eLife.61773	journal	December 2020
Structural basis of Stu2 recruitment to yeast kinetochores Zahm, Jacob A.; Stewart, Michael G.; Carrier, Joseph S. eLife, Vol. 10 https://doi.org/10.7554/eLife.65389	journal	February 2021
Three-dimensional structure of kinetochore-fibers in human mitotic spindles Kiewisz, Robert; Fabig, Gunar; Conway, William eLife, Vol. 11 https://doi.org/10.7554/eLife.75459	journal	July 2022

Similar Records

Molecular requirements for the formation of a kinetochore–microtubule interface by Dam1 and Ndc80 complexes

Journal Article · Sun Dec 30 19:00:00 EST 2012 · Journal of Cell Biology · OSTI ID:1625166

Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface

Journal Article · Thu May 03 20:00:00 EDT 2018 · Science · OSTI ID:1438840

Subunit organization in the Dam1 kinetochore complex and its ring around microtubules

Journal Article · Thu Sep 29 20:00:00 EDT 2011 · Molecular Biology of the Cell · OSTI ID:1625227

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Dam1 complex
Ndc80 complex
biochemistry & molecular biology
cell division
chromosome segregation
kinetochore
structure prediction

Structure of the Ndc80 complex and its interactions at the yeast kinetochore–microtubule interface

Citation Formats

References (69)

Similar Records

Related Subjects