6R8K

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Protein engineering expands the effector recognition profile of a rice NLR immune receptor.

De la Concepcion, J.C.Franceschetti, M.MacLean, D.Terauchi, R.Kamoun, S.Banfield, M.J.

(2019) Elife 8: --

  • DOI: 10.7554/eLife.47713
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plant NLR receptors detect pathogen effectors and initiate an immune response. Since their discovery, NLRs have been the focus of protein engineering to improve disease resistance. However, this has proven challenging, in part due to their narrow res ...

    Plant NLR receptors detect pathogen effectors and initiate an immune response. Since their discovery, NLRs have been the focus of protein engineering to improve disease resistance. However, this has proven challenging, in part due to their narrow response specificity. Previously, we revealed the structural basis of pathogen recognition by the integrated HMA of the rice NLR Pikp (Maqbool, Saitoh et al. 2015). Here, we used structure-guided engineering to expand the response profile of Pikp to variants of the rice blast pathogen effector AVR-Pik. A mutation located within an effector binding interface of the integrated Pikp-HMA domain increased the binding affinity for AVR-Pik variants in vitro and in vivo. This translates to an expanded cell death response to AVR-Pik variants previously unrecognized by Pikp in planta. Structures of the engineered Pikp-HMA in complex with AVR-Pik variants revealed the mechanism of expanded recognition. These results provide a proof-of-concept that protein engineering can improve the utility of plant NLR receptors where direct interaction between effectors and NLRs is established, particularly via integrated domains.


    Related Citations: 
    • Protein engineering expands the effector recognition profile of a rice NLR immune receptor
      De la Concepcion, J.C.,Franceschetti, M.,Terauchi, R.,Kamoun, S.,Banfield, M.J.
      (2019) Biorxiv --: --


    Organizational Affiliation

    The Sainsbury Laboratory, Norwich, United Kingdom.,Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom.,Division of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NBS-LRR class disease resistance protein Pikh-1
B
80Oryza sativa subsp. japonicaMutation(s): 0 
Gene Names: Pi-km1 (Pikh-1)
Find proteins for D5L9G5 (Oryza sativa subsp. japonica)
Go to UniProtKB:  D5L9G5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AVR-Pik protein
C
93Magnaporthe oryzaeMutation(s): 0 
Gene Names: AVR-Pik (AvrPik, Pikm, Pikp)
Find proteins for C4B8B8 (Magnaporthe oryzae)
Go to UniProtKB:  C4B8B8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 29.790α = 90.00
b = 65.330β = 90.00
c = 75.860γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004553
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P012574
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M02198X
European Research CouncilUnited Kingdom743165
Japan Society for the Promotion of ScienceJapanKAKENHI 15H05779

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection
  • Version 1.2: 2019-09-18
    Type: Data collection, Experimental preparation, Refinement description
  • Version 1.3: 2019-10-02
    Type: Data collection, Database references