7B1I | pdb_00007b1i

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with the HMA domain of OsHIPP19 from rice (Oryza sativa)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.233 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Multiple variants of the fungal effector AVR-Pik bind the HMA domain of the rice protein OsHIPP19, providing a foundation to engineer plant defense.

Maidment, J.H.R.Franceschetti, M.Maqbool, A.Saitoh, H.Jantasuriyarat, C.Kamoun, S.Terauchi, R.Banfield, M.J.

(2021) J Biological Chem 296: 100371-100371

  • DOI: https://doi.org/10.1016/j.jbc.2021.100371
  • Primary Citation Related Structures: 
    7B1I

  • PubMed Abstract: 

    Microbial plant pathogens secrete effector proteins, which manipulate the host to promote infection. Effectors can be recognized by plant intracellular nucleotide-binding leucine-rich repeat (NLR) receptors, initiating an immune response. The AVR-Pik effector from the rice blast fungus Magnaporthe oryzae is recognized by a pair of rice NLR receptors, Pik-1 and Pik-2. Pik-1 contains a noncanonical integrated heavy-metal-associated (HMA) domain, which directly binds AVR-Pik to activate plant defenses. The host targets of AVR-Pik are also HMA-domain-containing proteins, namely heavy-metal-associated isoprenylated plant proteins (HIPPs) and heavy-metal-associated plant proteins (HPPs). Here, we demonstrate that one of these targets interacts with a wider set of AVR-Pik variants compared with the Pik-1 HMA domains. We define the biochemical and structural basis of the interaction between AVR-Pik and OsHIPP19 and compare the interaction to that formed with the HMA domain of Pik-1. Using analytical gel filtration and surface plasmon resonance, we show that multiple AVR-Pik variants, including the stealthy variants AVR-PikC and AVR-PikF, which do not interact with any characterized Pik-1 alleles, bind to OsHIPP19 with nanomolar affinity. The crystal structure of OsHIPP19 in complex with AVR-PikF reveals differences at the interface that underpin high-affinity binding of OsHIPP19-HMA to a wider set of AVR-Pik variants than achieved by the integrated HMA domain of Pik-1. Our results provide a foundation for engineering the HMA domain of Pik-1 to extend binding to currently unrecognized AVR-Pik variants and expand disease resistance in rice to divergent pathogen strains.


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

Macromolecule Content 

  • Total Structure Weight: 19.19 kDa 
  • Atom Count: 1,294 
  • Modeled Residue Count: 155 
  • Deposited Residue Count: 172 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
OSIGBa0128P10.9 proteinA [auth B]78Oryza sativaMutation(s): 0 
Gene Names: OSIGBa0150F01.4OSIGBa0128P10.9
UniProt
Find proteins for Q01IL6 (Oryza sativa)
Explore Q01IL6 
Go to UniProtKB:  Q01IL6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01IL6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AVR-Pik proteinB [auth C]94Pyricularia oryzaeMutation(s): 0 
Gene Names: AVR-PikAvrPikPikmPikp
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: 1.90 Å
  • R-Value Free:  0.233 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.783α = 90
b = 53.782β = 90
c = 98.026γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2021-07-21
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary