Crystal structure of the unconventional kinetochore protein Perkinsela sp. KKT2a central domain

Experimental Data Snapshot

  • Resolution: 2.87 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

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Kinetoplastid kinetochore proteins KKT2 and KKT3 have unique centromere localization domains.

Marciano, G.Ishii, M.Nerusheva, O.O.Akiyoshi, B.

(2021) J Cell Biol 220

  • DOI: https://doi.org/10.1083/jcb.202101022
  • Primary Citation of Related Structures:  
    6TLX, 6TLY

  • PubMed Abstract: 

    The kinetochore is the macromolecular protein complex that assembles onto centromeric DNA and binds spindle microtubules. Evolutionarily divergent kinetoplastids have an unconventional set of kinetochore proteins. It remains unknown how kinetochores assemble at centromeres in these organisms. Here, we characterize KKT2 and KKT3 in the kinetoplastid parasite Trypanosoma brucei. In addition to the N-terminal kinase domain and C-terminal divergent polo boxes, these proteins have a central domain of unknown function. We show that KKT2 and KKT3 are important for the localization of several kinetochore proteins and that their central domains are sufficient for centromere localization. Crystal structures of the KKT2 central domain from two divergent kinetoplastids reveal a unique zinc-binding domain (termed the CL domain for centromere localization), which promotes its kinetochore localization in T. brucei. Mutations in the equivalent domain in KKT3 abolish its kinetochore localization and function. Our work shows that the unique central domains play a critical role in mediating the centromere localization of KKT2 and KKT3.

  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, Oxford, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein kinase131Perkinsela sp. CCAP 1560/4Mutation(s): 0 
Gene Names: XU18_4017
Find proteins for A0A0L1KLX8 (Perkinsela sp. CCAP 1560/4)
Explore A0A0L1KLX8 
Go to UniProtKB:  A0A0L1KLX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0L1KLX8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.87 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.845α = 90
b = 113.845β = 90
c = 46.013γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210622/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references