9S4Q | pdb_00009s4q

Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex lacking the Mis12c(Mtw1c) head 2 domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Assembly and phosphoregulatory mechanisms of the budding yeast outer kinetochore KMN complex.

Turner, N.N.Zhang, Z.Yang, J.Muir, K.W.McLaughlin, S.H.Morgan, T.Barford, D.

(2026) J Cell Biol 225

  • DOI: https://doi.org/10.1083/jcb.202506015
  • Primary Citation Related Structures: 
    9S4Q, 9S53, 9S5N

  • PubMed Abstract: 

    During mitosis and meiosis, kinetochores mediate interactions between chromosomes and spindle microtubules. Kinetochores are multi-megadalton protein complexes essential for chromosome segregation; however, recent structural, functional, and evolutionary studies have revealed divergent mechanisms of kinetochore assembly. Here, we use cryo-EM to understand the structural mechanisms by which the budding yeast microtubule-binding outer kinetochore KMN complex assembles, and how its interactions with the centromere-binding inner kinetochore are regulated. The KMN complex comprises three subcomplexes: Knl1c, Mis12cMtw1c, and Ndc80c. We show how C-terminal motifs of the Mis12cMtw1c subunits Dsn1, Mis12Mtw1, and Nnf1 bind Knl1c and Ndc80c. At the opposite end of the Mis12cMtw1c stalk, an N-terminal auto-inhibitory segment of Dsn1 (Dsn1AI) folds into two α-helices that engage the Mis12cMtw1c head 1 domain, thereby occluding binding sites for the inner kinetochore subunits CENP-CMif2 and CENP-UAme1, reducing their affinity for Mis12cMtw1. Our structure reveals how Aurora BIpl1 phosphorylation of Dsn1AI would release this auto-inhibition to substantially strengthen preexisting connections between the inner and outer kinetochore.


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology , Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 302.15 kDa 
  • Atom Count: 9,689 
  • Modeled Residue Count: 1,193 
  • Deposited Residue Count: 2,610 
  • Unique protein chains: 8

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinetochore-associated protein NNF1A [auth Nn]201Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NNF1YJR112WJ2011
UniProt
Find proteins for P47149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47149 
Go to UniProtKB:  P47149
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UniProt GroupP47149
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinetochore-associated protein MTW1B [auth Mt]289Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTW1DSN3NSL2YAL034W-AYAL034AW
UniProt
Find proteins for P39731 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39731 
Go to UniProtKB:  P39731
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UniProt GroupP39731
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer kinetochore KNL1 complex subunit KRE28C [auth Zw]420Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRE28YDR532C
UniProt
Find proteins for Q04431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04431 
Go to UniProtKB:  Q04431
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UniProt GroupQ04431
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer kinetochore KNL1 complex subunit SPC105D [auth Kl]474Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPC105KNL1YGL093W
UniProt
Find proteins for P53148 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P53148
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UniProt GroupP53148
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinetochore-associated protein DSN1E [auth Ds]576Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DSN1YIR010WYIB10W
UniProt
Find proteins for P40568 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40568
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinetochore protein SPC24F [auth 24]213Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPC24YMR117CYM9718.16C
UniProt
Find proteins for Q04477 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinetochore protein SPC25G [auth 25]221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPC25YER018C
UniProt
Find proteins for P40014 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40014
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinetochore-associated protein NSL1H [auth Ns]216Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NSL1YPL233W
UniProt
Find proteins for Q12143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12143 
Go to UniProtKB:  Q12143
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UniProt GroupQ12143
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:
RECONSTRUCTIONRELION5

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC576/A25675
Cancer Research UKUnited KingdomC576/A14109
UK Research and Innovation (UKRI)United KingdomMC_UP_1201/6

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-08
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Data collection, Database references