7BNT | pdb_00007bnt

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with a predicted ancestral HMA domain of Pik-1 from Oryza spp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 
    0.184 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.145 (Depositor) 
  • R-Value Observed: 
    0.147 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7BNT

This is version 1.3 of the entry. See complete history

Literature

Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain.

Bialas, A.Langner, T.Harant, A.Contreras, M.P.Stevenson, C.E.Lawson, D.M.Sklenar, J.Kellner, R.Moscou, M.J.Terauchi, R.Banfield, M.J.Kamoun, S.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.66961
  • Primary Citation Related Structures: 
    7BNT

  • PubMed Abstract: 

    A subset of plant NLR immune receptors carry unconventional integrated domains in addition to their canonical domain architecture. One example is rice Pik-1 that comprises an integrated heavy metal-associated (HMA) domain. Here, we reconstructed the evolutionary history of Pik-1 and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA domain. Phylogenetic analyses revealed that the HMA domain integrated into Pik-1 before Oryzinae speciation over 15 million years ago and has been under diversifying selection. Ancestral sequence reconstruction coupled with functional studies showed that two Pik-1 allelic variants independently evolved from a weakly binding ancestral state to high-affinity binding of the blast fungus effector AVR-PikD. We conclude that for most of its evolutionary history the Pik-1 HMA domain did not sense AVR-PikD, and that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes. These findings highlight the dynamic nature of the evolutionary mechanisms underpinning NLR adaptation to plant pathogens.


  • Organizational Affiliation
    • The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 26.57 kDa 
  • Atom Count: 2,054 
  • Modeled Residue Count: 230 
  • Deposited Residue Count: 244 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Predicted ancestral HMA domain of Pik-1 from Oryza spp.
A, B
75synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AVR-Pik protein94Pyricularia 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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free:  0.184 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.145 (Depositor) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.486α = 90
b = 119.486β = 90
c = 35.974γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata reduction
DIALSdata reduction
DIALSdata scaling
REFMACphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Belgium743165
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M011216/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P012574/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary