9EMY | pdb_00009emy

P. falciparum FIKK13 in complex with ATPgammaS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.286 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.242 (DCC) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound.

Belda, H.Bradley, D.Christodoulou, E.Nofal, S.D.Broncel, M.Jones, D.Davies, H.Bertran, M.T.Purkiss, A.G.Ogrodowicz, R.W.Joshi, D.O'Reilly, N.Walport, L.Powell, A.House, D.Kjaer, S.Claessens, A.Landry, C.R.Treeck, M.

(2025) Nat Microbiol 10: 1463-1483

  • DOI: https://doi.org/10.1038/s41564-025-02017-4
  • Primary Citation of Related Structures:  
    9EMY

  • PubMed Abstract: 

    Of 250 Plasmodium species, 6 infect humans, with P. falciparum causing over 95% of 600,000 annual malaria-related deaths. Its pathology arises from host cell remodelling driven by over 400 exported parasite proteins, including the FIKK kinase family. About one million years ago, a bird-infecting Plasmodium species crossed into great apes and a single non-exported FIKK kinase gained an export element. This led to a rapid expansion into 15-21 atypical, exported Ser/Thr effector kinases. Here, using genomic and proteomic analyses, we demonstrate FIKK differentiation via changes in subcellular localization, expression timing and substrate motifs, which supports an individual important role in host-pathogen interactions. Structural data and AlphaFold2 predictions reveal fast-evolving loops in the kinase domain that probably enabled rapid functional diversification for substrate preferences. One FIKK evolved exclusive tyrosine phosphorylation, previously thought absent in Plasmodium. Despite divergence of substrate preferences, the atypical ATP binding pocket is conserved and we identified a single compound that inhibits all FIKKs. A pan-specific inhibitor could reduce resistance development and improve malaria control strategies.


  • Organizational Affiliation
    • Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
non-specific serine/threonine protein kinase
A, B, G, H
413Plasmodium falciparumMutation(s): 0 
Gene Names: CK202_4380CYL21_5595
EC: 2.7.11.1
UniProt
Find proteins for A0A2I0BRS6 (Plasmodium falciparum (isolate NF54))
Explore A0A2I0BRS6 
Go to UniProtKB:  A0A2I0BRS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2I0BRS6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 9F10
C, D, I, J
136Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 2G9
E, F, K, L
134Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.286 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.242 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.397α = 90
b = 121.657β = 90.02
c = 151.059γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-10-08
    Changes: Database references