7A8X

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikC with the HMA domain of Pikh-1 from rice (Oryza sativa)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The allelic rice immune receptor Pikh confers extended resistance to strains of the blast fungus through a single polymorphism in the effector binding interface.

De la Concepcion, J.C.Maidment, J.H.R.Longya, A.Xiao, G.Franceschetti, M.Banfield, M.J.

(2021) PLoS Pathog 17: e1009368-e1009368

  • DOI: https://doi.org/10.1371/journal.ppat.1009368
  • Primary Citation of Related Structures:  
    7A8W, 7A8X

  • PubMed Abstract: 

    Arms race co-evolution drives rapid adaptive changes in pathogens and in the immune systems of their hosts. Plant intracellular NLR immune receptors detect effectors delivered by pathogens to promote susceptibility, activating an immune response that halts colonization. As a consequence, pathogen effectors evolve to escape immune recognition and are highly variable. In turn, NLR receptors are one of the most diverse protein families in plants, and this variability underpins differential recognition of effector variants. The molecular mechanisms underlying natural variation in effector recognition by NLRs are starting to be elucidated. The rice NLR pair Pik-1/Pik-2 recognizes AVR-Pik effectors from the blast fungus Magnaporthe oryzae, triggering immune responses that limit rice blast infection. Allelic variation in a heavy metal associated (HMA) domain integrated in the receptor Pik-1 confers differential binding to AVR-Pik variants, determining resistance specificity. Previous mechanistic studies uncovered how a Pik allele, Pikm, has extended recognition to effector variants through a specialized HMA/AVR-Pik binding interface. Here, we reveal the mechanistic basis of extended recognition specificity conferred by another Pik allele, Pikh. A single residue in Pikh-HMA increases binding to AVR-Pik variants, leading to an extended effector response in planta. The crystal structure of Pikh-HMA in complex with an AVR-Pik variant confirmed that Pikh and Pikm use a similar molecular mechanism to extend their pathogen recognition profile. This study shows how different NLR receptor alleles functionally converge to extend recognition specificity to pathogen effectors.


  • Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NBS-LRR class disease resistance protein
A, B, D, E
78Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Pi-km1Pikh-1
UniProt
Find proteins for D5L9G5 (Oryza sativa subsp. japonica)
Explore D5L9G5 
Go to UniProtKB:  D5L9G5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5L9G5
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 protein
C, F
93Pyricularia oryzae 70-15Mutation(s): 0 
Gene Names: MGG_15972
UniProt
Find proteins for G4MXW3 (Pyricularia oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958))
Explore G4MXW3 
Go to UniProtKB:  G4MXW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG4MXW3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.351α = 90
b = 83.121β = 90
c = 107.842γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
Aimlessdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M011216/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P012574
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M02198X
European Research Council (ERC)United Kingdom743165
John Innes FoundationUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description