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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kinetochore protein SPC25 A, C90Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPC25, YER018C
Find proteins for P40014 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P40014
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Kinetochore protein SPC24 B, D66Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPC24, YM9718.16C, YMR117C
Find proteins for Q04477 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q04477
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Kinetochore-associated protein CNN1 E, F25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CNN1, YFR046C
Find proteins for P43618 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43618 
Go to UniProtKB:  P43618
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
B, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
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