9QK5 | pdb_00009qk5

X-ray crystal structure of SlPYL1-Caffeic Acid complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Natural modulators of abscisic acid Signaling: Insights into polyphenol-based antagonists and their role in ABA receptor regulation.

Merino, J.Rivera-Moreno, M.Bono, M.Nunez-Villanueva, D.Gonzalez-Vega, A.Mayordomo, C.Infantes, L.Chikhale, R.Rodriguez, P.L.Albert, A.

(2025) Plant Physiol Biochem 227: 110155-110155

  • DOI: https://doi.org/10.1016/j.plaphy.2025.110155
  • Primary Citation of Related Structures:  
    9QK3, 9QK4, 9QK5, 9QK6

  • PubMed Abstract: 

    The phytohormone abscisic acid (ABA) plays a pivotal role in regulating essential plant processes, including seed dormancy, germination, and stress responses. ABA signaling is mediated by PYR/PYL/RCAR receptors, which interact with clade A PP2C phosphatases to control downstream signaling pathways. Advances in structural biology have enabled the development of synthetic ABA modulators, such as agonists and antagonists, which can enhance or inhibit ABA signaling for agricultural applications. However, the high production costs and potential toxicity of synthetic modulators have motivated the search for natural alternatives. Here, we explore the potential of polyphenols, a class of plant secondary metabolites, as eco-friendly non-canonical ligands for ABA receptors. Through virtual screening and structural analysis, we identified coumaric acid and other hydroxycinnamic acids as natural ABA antagonists. These compounds compete with ABA for receptor binding, disrupting the ABA-dependent inhibition of PP2C phosphatases by PYR/PYL proteins. As a result, they counteract ABA-imposed stress responses in Arabidopsis thaliana, promoting seed germination and seedling establishment. Further chemical optimization yielded improved ABA antagonists based on hydroxycinnamic acid and natural amino acid conjugates. Their use in plants provides a sustainable alternative to synthetic modulators and opens new biotechnological strategies for crop management. In addition, our findings highlight a mechanism for fine-tuning ABA receptor activity in vivo through the interaction of ABA receptors with endogenous hydroxycinnamic acids.


  • Organizational Affiliation

    Instituto de Química-Física "Blas Cabrera" (IQF) Consejo Superior de Investigaciones Científicas, ES-28006, Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SlPYL1-NIO232Solanum lycopersicumMutation(s): 0 
Gene Names: 101268417
UniProt
Find proteins for A0A3Q7HTY9 (Solanum lycopersicum)
Explore A0A3Q7HTY9 
Go to UniProtKB:  A0A3Q7HTY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3Q7HTY9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.066α = 90
b = 90.066β = 90
c = 51.402γ = 120
Software Package:
Software NamePurpose
autoPROCdata reduction
autoPROCdata scaling
PHENIXrefinement
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-119805RB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release