9GNL | pdb_00009gnl

X-ray crystal structure of VvPYL1 with ABA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.306 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.235 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Chemical activation of ABA signaling in grapevine through the iSB09 and AMF4 ABA receptor agonists enhances water use efficiency.

Bono, M.Ferrer-Gallego, R.Pou, A.Rivera-Moreno, M.Benavente, J.L.Mayordomo, C.Deis, L.Carbonell-Bejerano, P.Pizzio, G.A.Navarro-Paya, D.Matus, J.T.Martinez-Zapater, J.M.Albert, A.Intrigliolo, D.S.Rodriguez, P.L.

(2024) Physiol Plant 176: e14635-e14635

  • DOI: https://doi.org/10.1111/ppl.14635
  • Primary Citation of Related Structures:  
    9GNL, 9GNM

  • PubMed Abstract: 

    Grapevine (Vitis vinifera L.) is the world's third most valuable horticultural crop, and the current environmental scenario is massively shifting the grape cultivation landscape. The increase in heatwaves and drought episodes alter fruit ripening, compromise grape yield and vine survival, intensifying the pressure on using limited water resources. ABA is a key phytohormone that reduces canopy transpiration and helps plants to cope with water deficit. However, the exogenous application of ABA is impractical because it suffers fast catabolism, and UV-induced isomerization abolishes its bioactivity. Consequently, there is an emerging field for developing molecules that act as ABA receptor agonists and modulate ABA signaling but have a longer half-life. We have explored the foliar application of the iSB09 and AMF4 agonists in the two grapevine cultivars cv. 'Bobal' and 'Tempranillo' to induce an ABA-like response to facilitate plant adaptation to drought. The results indicate that iSB09 and AMF4 act through the VviPYL1-like, VviPYL4-like, and VviPYL8-like ABA receptors to trigger stomatal closure, reduce plant transpiration, and increase water use efficiency. Structural and bioinformatic analysis of VviPYL1 in complex with ABA or these agonists revealed key structural determinants for efficient ligand binding, providing a mechanistic framework to understand receptor activation by the ligands. Physiological analyses further demonstrated that iSB09 has a more sustained effect on reducing transpiration than ABA, and agonist spraying of grapevine leaves protected PSII during drought stress. These findings offer innovative approaches to strengthen the vine's response to water stress and reduce plant consumptive water use under limited soil water conditions.


  • Organizational Affiliation
    • Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Abscisic acid receptor PYR1
A, B
214Escherichia coliMutation(s): 0 
Gene Names: VIT_02s0012g01270
UniProt
Find proteins for F6HT94 (Vitis vinifera)
Explore F6HT94 
Go to UniProtKB:  F6HT94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF6HT94
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A8S (Subject of Investigation/LOI)
Query on A8S

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
C15 H20 O4
JLIDBLDQVAYHNE-YKALOCIXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.306 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.235 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.535α = 90
b = 49.621β = 99.725
c = 65.95γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report



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: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Structure summary
  • Version 1.2: 2025-10-29
    Changes: Database references