7XEY

EDS1-PAD4 complexed with pRib-ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Identification and receptor mechanism of TIR-catalyzed small molecules in plant immunity.

Huang, S.Jia, A.Song, W.Hessler, G.Meng, Y.Sun, Y.Xu, L.Laessle, H.Jirschitzka, J.Ma, S.Xiao, Y.Yu, D.Hou, J.Liu, R.Sun, H.Liu, X.Han, Z.Chang, J.Parker, J.E.Chai, J.

(2022) Science 377: eabq3297-eabq3297

  • DOI: https://doi.org/10.1126/science.abq3297
  • Primary Citation of Related Structures:  
    7XDD, 7XEY

  • PubMed Abstract: 

    Plant nucleotide-binding leucine-rich repeat-containing (NLR) receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain sense pathogen effectors to enable TIR-encoded nicotinamide adenine dinucleotide hydrolase (NADase) activity for immune signaling. TIR-NLR signaling requires the helper NLRs N requirement gene 1 (NRG1), Activated Disease Resistance 1 (ADR1), and Enhanced Disease Susceptibility 1 (EDS1), which forms a heterodimer with each of its paralogs Phytoalexin Deficient 4 (PAD4) and Senescence-Associated Gene 101 (SAG101). Here, we show that TIR-containing proteins catalyze the production of 2'-(5''-phosphoribosyl)-5'-adenosine monophosphate (pRib-AMP) and diphosphate (pRib-ADP) in vitro and in planta. Biochemical and structural data demonstrate that EDS1-PAD4 is a receptor complex for pRib-AMP and pRib-ADP, which allosterically promote EDS1-PAD4 interaction with ADR1-L1 but not NRG1A. Our study identifies TIR-catalyzed pRib-AMP and pRib-ADP as a missing link in TIR signaling through EDS1-PAD4 and as likely second messengers for plant immunity.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein EDS1623Arabidopsis thalianaMutation(s): 0 
Gene Names: EDS1EDS1-90EDS1AAt3g48090T17F15.40
UniProt
Find proteins for Q9SU72 (Arabidopsis thaliana)
Explore Q9SU72 
Go to UniProtKB:  Q9SU72
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SU72
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lipase-like PAD4541Arabidopsis thalianaMutation(s): 0 
Gene Names: PAD4EDS9At3g52430F22O6.190
EC: 2.3.1
UniProt
Find proteins for Q9S745 (Arabidopsis thaliana)
Explore Q9S745 
Go to UniProtKB:  Q9S745
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S745
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.357α = 90
b = 91.863β = 111.79
c = 94.271γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2022-08-10
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description