4GEQ

Crystal structure of the Spc24-Spc25/Cnn1 binding interface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A structural basis for kinetochore recruitment of the Ndc80 complex via two distinct centromere receptors.

Malvezzi, F.Litos, G.Schleiffer, A.Heuck, A.Mechtler, K.Clausen, T.Westermann, S.

(2013) EMBO J 32: 409-423

  • DOI: https://doi.org/10.1038/emboj.2012.356
  • Primary Citation of Related Structures:  
    4GEQ

  • PubMed Abstract: 

    The Ndc80 complex is the key microtubule-binding element of the kinetochore. In contrast to the well-characterized interaction of Ndc80-Nuf2 heads with microtubules, little is known about how the Spc24-25 heterodimer connects to centromeric chromatin. Here, we present molecular details of Spc24-25 in complex with the histone-fold protein Cnn1/CENP-T illustrating how this connection ultimately links microtubules to chromosomes. The conserved Ndc80 receptor motif of Cnn1 is bound as an α helix in a hydrophobic cleft at the interface between Spc24 and Spc25. Point mutations that disrupt the Ndc80-Cnn1 interaction also abrogate binding to the Mtw1 complex and are lethal in yeast. We identify a Cnn1-related motif in the Dsn1 subunit of the Mtw1 complex, necessary for Ndc80 binding and essential for yeast growth. Replacing this region with the Cnn1 peptide restores viability demonstrating functionality of the Ndc80-binding module in different molecular contexts. Finally, phosphorylation of the Cnn1 N-terminus coordinates the binding of the two competing Ndc80 interaction partners. Together, our data provide structural insights into the modular binding mechanism of the Ndc80 complex to its centromere recruiters.


  • Organizational Affiliation

    Research Institute of Molecular Pathology IMP, Vienna 1030, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinetochore protein SPC25
A, C
90Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPC25YER018C
UniProt
Find proteins for P40014 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40014 
Go to UniProtKB:  P40014
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40014
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Kinetochore protein SPC24
B, D
66Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPC24YM9718.16CYMR117C
UniProt
Find proteins for Q04477 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04477 
Go to UniProtKB:  Q04477
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04477
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Kinetochore-associated protein CNN1
E, F
25Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P43618 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43618 
Go to UniProtKB:  P43618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43618
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.142α = 90
b = 61.848β = 90
c = 139.056γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
PHENIXrefinement
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-02-20
    Changes: Database references
  • Version 1.2: 2015-07-01
    Changes: Data collection
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description