Structure of the budding yeast Ndc10 N-terminal domain

Experimental Data Snapshot

  • Resolution: 1.89 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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The Structure of the Yeast Kinetochore Ndc10 DNA-Binding Domain Reveals an Unexpected Evolutionary Relationship to Tyrosine Recombinases.

Perriches, T.Singleton, M.R.

(2012) J Biol Chem 287: 5173

  • DOI: https://doi.org/10.1074/jbc.C111.318501
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We have solved the x-ray structure of the N-terminal half of the yeast kinetochore protein Ndc10 at 1.9 Å resolution. This essential protein is a key constituent of the budding yeast centromere and is essential for the recruitment of the centromeric nucleosome and establishment of the kinetochore. The fold of the protein shows unexpected similarities to the tyrosine recombinase/λ-integrase family of proteins, most notably Cre, with some variation in the relative position of the subdomains. This finding offers new insights into kinetochore evolution and the adaptation of a well studied protein fold to a novel role. By comparison with tyrosine recombinases and mutagenesis studies, we have been able to define some of the key DNA-binding motifs.

  • Organizational Affiliation

    Macromolecular Structure and Function Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT A956Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P32504 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32504 
Go to UniProtKB:  P32504
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32504
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.89 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.74α = 90
b = 87.76β = 90
c = 104.57γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2012-01-25
    Changes: Other
  • Version 1.2: 2012-02-29
    Changes: Other
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Other