7BNT

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with a predicted ancestral HMA domain of Pik-1 from Oryza spp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain.

Bialas, A.Langner, T.Harant, A.Contreras, M.P.Stevenson, C.E.Lawson, D.M.Sklenar, J.Kellner, R.Moscou, M.J.Terauchi, R.Banfield, M.J.Kamoun, S.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.66961
  • Primary Citation of Related Structures:  
    7BNT

  • PubMed Abstract: 

    A subset of plant NLR immune receptors carry unconventional integrated domains in addition to their canonical domain architecture. One example is rice Pik-1 that comprises an integrated heavy metal-associated (HMA) domain. Here, we reconstructed the evolutionary history of Pik-1 and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA domain. Phylogenetic analyses revealed that the HMA domain integrated into Pik-1 before Oryzinae speciation over 15 million years ago and has been under diversifying selection. Ancestral sequence reconstruction coupled with functional studies showed that two Pik-1 allelic variants independently evolved from a weakly binding ancestral state to high-affinity binding of the blast fungus effector AVR-PikD. We conclude that for most of its evolutionary history the Pik-1 HMA domain did not sense AVR-PikD, and that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes. These findings highlight the dynamic nature of the evolutionary mechanisms underpinning NLR adaptation to plant pathogens.


  • Organizational Affiliation

    The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Predicted ancestral HMA domain of Pik-1 from Oryza spp.
A, B
75synthetic constructMutation(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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AVR-Pik protein94Pyricularia oryzaeMutation(s): 0 
Gene Names: AVR-PikAvrPikPikmPikp
UniProt
Find proteins for C4B8B8 (Pyricularia oryzae)
Explore C4B8B8 
Go to UniProtKB:  C4B8B8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4B8B8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.486α = 90
b = 119.486β = 90
c = 35.974γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata reduction
DIALSdata reduction
DIALSdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Belgium743165
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M011216/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P012574/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description