6WPG

Structural Basis of Salicylic Acid Perception by Arabidopsis NPR Proteins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

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This is version 1.3 of the entry. See complete history


Literature

Structural basis of salicylic acid perception by Arabidopsis NPR proteins.

Wang, W.Withers, J.Li, H.Zwack, P.J.Rusnac, D.V.Shi, H.Liu, L.Yan, S.Hinds, T.R.Guttman, M.Dong, X.Zheng, N.

(2020) Nature 586: 311-316

  • DOI: https://doi.org/10.1038/s41586-020-2596-y
  • Primary Citation of Related Structures:  
    6WPG

  • PubMed Abstract: 

    Salicylic acid (SA) is a plant hormone that is critical for resistance to pathogens 1-3 . The NPR proteins have previously been identified as SA receptors 4-10 , although how they perceive SA and coordinate hormonal signalling remain unknown. Here we report the mapping of the SA-binding core of Arabidopsis thaliana NPR4 and its ligand-bound crystal structure. The SA-binding core domain of NPR4 refolded with SA adopts an α-helical fold that completely buries SA in its hydrophobic core. The lack of a ligand-entry pathway suggests that SA binding involves a major conformational remodelling of the SA-binding core of NPR4, which we validated using hydrogen-deuterium-exchange mass spectrometry analysis of the full-length protein and through SA-induced disruption of interactions between NPR1 and NPR4. We show that, despite the two proteins sharing nearly identical hormone-binding residues, NPR1 displays minimal SA-binding activity compared to NPR4. We further identify two surface residues of the SA-binding core, the mutation of which can alter the SA-binding ability of NPR4 and its interaction with NPR1. We also demonstrate that expressing a variant of NPR4 that is hypersensitive to SA could enhance SA-mediated basal immunity without compromising effector-triggered immunity, because the ability of this variant to re-associate with NPR1 at high levels of SA remains intact. By revealing the structural mechanisms of SA perception by NPR proteins, our work paves the way for future investigation of the specific roles of these proteins in SA signalling and their potential for engineering plant immunity.


  • Organizational Affiliation

    Department of Pharmacology, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory protein NPR4
A, B
177Arabidopsis thalianaMutation(s): 0 
Gene Names: NPR4At4g19660T16H5.20
UniProt
Find proteins for Q5ICL9 (Arabidopsis thaliana)
Explore Q5ICL9 
Go to UniProtKB:  Q5ICL9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ICL9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.293α = 90
b = 88.293β = 90
c = 138.003γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references