5A6W

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikp1 from rice (Oryza sativa)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of pathogen recognition by an integrated HMA domain in a plant NLR immune receptor.

Maqbool, A.Saitoh, H.Franceschetti, M.Stevenson, C.E.Uemura, A.Kanzaki, H.Kamoun, S.Terauchi, R.Banfield, M.J.

(2015) Elife 4

  • DOI: https://doi.org/10.7554/eLife.08709
  • Primary Citation of Related Structures:  
    5A6P, 5A6W

  • PubMed Abstract: 

    Plants have evolved intracellular immune receptors to detect pathogen proteins known as effectors. How these immune receptors detect effectors remains poorly understood. Here we describe the structural basis for direct recognition of AVR-Pik, an effector from the rice blast pathogen, by the rice intracellular NLR immune receptor Pik. AVR-PikD binds a dimer of the Pikp-1 HMA integrated domain with nanomolar affinity. The crystal structure of the Pikp-HMA/AVR-PikD complex enabled design of mutations to alter protein interaction in yeast and in vitro, and perturb effector-mediated response both in a rice cultivar containing Pikp and upon expression of AVR-PikD and Pikp in the model plant Nicotiana benthamiana. These data reveal the molecular details of a recognition event, mediated by a novel integrated domain in an NLR, which initiates a plant immune response and resistance to rice blast disease. Such studies underpin novel opportunities for engineering disease resistance to plant pathogens in staple food crops.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RESISTANCE PROTEIN PIKP-1
A, B
75Oryza sativaMutation(s): 0 
UniProt
Find proteins for E9KPB5 (Oryza sativa subsp. japonica)
Explore E9KPB5 
Go to UniProtKB:  E9KPB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9KPB5
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 PROTEIN93Pyricularia oryzaeMutation(s): 0 
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: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.41α = 90
b = 118.41β = 90
c = 35.81γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Database references
  • Version 1.2: 2017-03-22
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description