7QZD

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with an engineered HMA domain of Pikp-1 (Pikp-SNK-EKE) from rice (Oryza sativa)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor.

Maidment, J.H.R.Shimizu, M.Bentham, A.R.Vera, S.Franceschetti, M.Longya, A.Stevenson, C.E.M.De la Concepcion, J.C.Bialas, A.Kamoun, S.Terauchi, R.Banfield, M.J.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.81123
  • Primary Citation of Related Structures:  
    7QPX, 7QZD

  • PubMed Abstract: 

    A subset of plant intracellular NLR immune receptors detect effector proteins, secreted by phytopathogens to promote infection, through unconventional integrated domains which resemble the effector's host targets. Direct binding of effectors to these integrated domains activates plant defenses. The rice NLR receptor Pik-1 binds the Magnaporthe oryzae effector AVR-Pik through an integrated heavy metal-associated (HMA) domain. However, the stealthy alleles AVR-PikC and AVR-PikF avoid interaction with Pik-HMA and evade host defenses. Here, we exploited knowledge of the biochemical interactions between AVR-Pik and its host target, OsHIPP19, to engineer novel Pik-1 variants that respond to AVR-PikC/F. First, we exchanged the HMA domain of Pikp-1 for OsHIPP19-HMA, demonstrating that effector targets can be incorporated into NLR receptors to provide novel recognition profiles. Second, we used the structure of OsHIPP19-HMA to guide the mutagenesis of Pikp-HMA to expand its recognition profile. We demonstrate that the extended recognition profiles of engineered Pikp-1 variants correlate with effector binding in planta and in vitro, and with the gain of new contacts across the effector/HMA interface. Crucially, transgenic rice producing the engineered Pikp-1 variants was resistant to blast fungus isolates carrying AVR-PikC or AVR-PikF. These results demonstrate that effector target-guided engineering of NLR receptors can provide new-to-nature disease resistance in 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-1A,
B,
D [auth E],
E [auth F]
80Oryza sativa Japonica GroupMutation(s): 3 
Gene Names: Pikp-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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Avr-PikC,
F [auth G]
93Pyricularia oryzaeMutation(s): 0 
UniProt
Find proteins for A0A219T3Y8 (Pyricularia oryzae)
Explore A0A219T3Y8 
Go to UniProtKB:  A0A219T3Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A219T3Y8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.381α = 90
b = 80.782β = 90
c = 103.804γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)JapanBB/M011216/1
Biotechnology and Biological Sciences Research Council (BBSRC)JapanBB/P012574
Biotechnology and Biological Sciences Research Council (BBSRC)JapanBBS/E/J/000PR9795
Biotechnology and Biological Sciences Research Council (BBSRC)JapanBB/M02198X
European Research Council (ERC)Japan743165
The Thailand Research Fund (TRF)JapanPHD/0152/2556
John Innes FoundationJapan--
Japan Society for the Promotion of Science (JSPS)JapanKAKENHI 15H05779
Japan Society for the Promotion of Science (JSPS)JapanKAKENHI 20H00421

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2023-05-31
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description