6Q6Z

Structure of the plant immune signaling node EDS1 (enhanced disease susceptibility 1) in complex with nanobody ENB21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Arabidopsis immunity regulator EDS1 in a PAD4/SAG101-unbound form is a monomer with an inherently inactive conformation.

Voss, M.Toelzer, C.Bhandari, D.D.Parker, J.E.Niefind, K.

(2019) J Struct Biol 208: 107390-107390

  • DOI: https://doi.org/10.1016/j.jsb.2019.09.007
  • Primary Citation of Related Structures:  
    6I8G, 6I8H, 6Q6Z

  • PubMed Abstract: 

    In plant innate immunity, enhanced disease susceptibility 1 (EDS1) integrates all pathogen-induced signals transmitted by TIR-type NLR receptors. Driven by an N-terminal α/β-hydrolase-fold domain with a protruding interaction helix, EDS1 assembles with two homologs, phytoalexin-deficient 4 (PAD4) and senescence-associated gene 101 (SAG101). The resulting heterodimers are critical for EDS1 function and structurally well characterized. Here, we resolve solution and crystal structures of unbound Arabidopsis thaliana EDS1 (AtEDS1) using nanobodies for crystallization. These structures, together with gel filtration and immunoprecipitation data, show that PAD4/SAG101-unbound AtEDS1 is stable as a monomer and does not form the homodimers recorded in public databases. Its PAD4/SAG101 anchoring helix is disordered unless engaged in protein/protein interactions. As in the complex with SAG101, monomeric AtEDS1 has a substrate-inaccessible esterase triad with a blocked oxyanion hole and without space for a covalent acyl intermediate. These new structures suggest that the AtEDS1 monomer represents an inactive or pre-activated ground state.


  • Organizational Affiliation

    University of Cologne, Department of Chemistry, Institute of Biochemistry, Zülpicher Str. 47, D-50674 Cologne, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein EDS1L631Arabidopsis thalianaMutation(s): 0 
Gene Names: EDS1
UniProt
Find proteins for Q9XF23 (Arabidopsis thaliana)
Explore Q9XF23 
Go to UniProtKB:  Q9XF23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XF23
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EDS1-SPECIFIC NANOBODY142Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.192α = 90
b = 142.192β = 90
c = 97.802γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyNI 643/6-1

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description