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 

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

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kinetochore protein SPC25
A, C
90Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SPC25
Find proteins for P40014 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SPC25
Go to UniProtKB:  P40014
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Kinetochore protein SPC24
B, D
66Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SPC24
Find proteins for Q04477 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SPC24
Go to UniProtKB:  Q04477
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Kinetochore-associated protein CNN1
E, F
25Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CNN1
Find proteins for P43618 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CNN1
Go to UniProtKB:  P43618
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.142α = 90.00
b = 61.848β = 90.00
c = 139.056γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
BUSTERrefinement
MxCuBEdata collection
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Database references
  • Version 1.2: 2015-07-01
    Type: Data collection
  • Version 1.3: 2018-03-07
    Type: Data collection