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: 1.60 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

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:  
    6R8K, 6R8M

  • PubMed Abstract: 
  • Plant nucleotide binding, leucine-rich repeat (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 approach has proven challenging, in part due to their narrow response specificity ...

    Plant nucleotide binding, leucine-rich repeat (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 approach has proven challenging, in part due to their narrow response specificity. Previously, we revealed the structural basis of pathogen recognition by the integrated heavy metal associated (HMA) domain of the rice NLR Pikp (Maqbool 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. The 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 where this interaction occurs 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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NBS-LRR class disease resistance protein Pikh-1A [auth B]80Oryza 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AVR-Pik proteinB [auth C]93Pyricularia oryzaeMutation(s): 0 
Gene Names: AVR-PikAvrPikPikmPikp
UniProt
Find proteins for C4B8B8 (Magnaporthe oryzae)
Explore C4B8B8 
Go to UniProtKB:  C4B8B8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4B8B8
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.79α = 90
b = 65.33β = 90
c = 75.86γ = 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 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  (Full details and data files)

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