6FU9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen.

De la Concepcion, J.C.Franceschetti, M.Maqbool, A.Saitoh, H.Terauchi, R.Kamoun, S.Banfield, M.J.

(2018) Nat Plants 4: 576-585

  • DOI: https://doi.org/10.1038/s41477-018-0194-x
  • Primary Citation of Related Structures:  
    6FU9, 6FUB, 6FUD, 6G10, 6G11

  • PubMed Abstract: 

    Accelerated adaptive evolution is a hallmark of plant-pathogen interactions. Plant intracellular immune receptors (NLRs) often occur as allelic series with differential pathogen specificities. The determinants of this specificity remain largely unknown. Here, we unravelled the biophysical and structural basis of expanded specificity in the allelic rice NLR Pik, which responds to the effector AVR-Pik from the rice blast pathogen Magnaporthe oryzae. Rice plants expressing the Pikm allele resist infection by blast strains expressing any of three AVR-Pik effector variants, whereas those expressing Pikp only respond to one. Unlike Pikp, the integrated heavy metal-associated (HMA) domain of Pikm binds with high affinity to each of the three recognized effector variants, and variation at binding interfaces between effectors and Pikp-HMA or Pikm-HMA domains encodes specificity. By understanding how co-evolution has shaped the response profile of an allelic NLR, we highlight how natural selection drove the emergence of new receptor specificities. This work has implications for the engineering of NLRs with improved utility in agriculture.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NBS-LRR class disease resistance protein
A, C
81Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Pikm1-TSPi-km1
UniProt
Find proteins for B5UBC1 (Oryza sativa subsp. japonica)
Explore B5UBC1 
Go to UniProtKB:  B5UBC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5UBC1
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
B, D
93Pyricularia oryzaeMutation(s): 0 
Gene Names: AVR-PikAvrPikPikmPikp
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.09α = 90
b = 87.13β = 90
c = 103.84γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J00453
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P012574
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M02198X
European Research Council743165
Japan Society for the Promotion of ScienceJapanKAKENHI 15H05779

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description