9H0I | pdb_00009h0i

X-RAY CRYSTAL STRUCTURE OF THE CsPYL1-iCB-HAB1 TERNARY COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.213 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into ABA receptor agonists reveal critical features to optimize and design a broad-spectrum ABA signaling activator.

Bono, M.Mayordomo, C.Coego, A.Illescas-Miranda, J.Rivera-Moreno, M.Infantes, L.Lopez-Carracedo, P.Sanchez-Olvera, M.Martin-Vasquez, C.Pizzio, G.A.Merino, J.Forment, J.Merilo, E.Estevez, J.C.Albert, A.Rodriguez, P.L.

(2025) Mol Plant 18: 1526-1548

  • DOI: https://doi.org/10.1016/j.molp.2025.07.014
  • Primary Citation of Related Structures:  
    9H0H, 9H0I, 9H0J

  • PubMed Abstract: 

    Crop yield is at risk due to water scarcity and climate change. Using agrochemicals to activate hormone receptors can help regulate transpiration and modulate transcription to address water deficits. Structure-guided optimization of the multiple abscisic acid (ABA) receptor-agonist interactions is required to activate efficiently the entire PYRABACTIN RESISTANCE 1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS (RCAR) receptor family. The new agonist iCB, generated through scaffold-merging led by X-ray structure, activates subfamily II and III at low nM concentrations and subfamily I receptors at higher nM concentrations. Structural analysis of opabactin and iCB ternary complexes illuminates selectivity-determining residues, making PYL1/PYL4/PYL8 subfamilies sensitive to specific agonists, revealing differential sensitivity of receptor subfamilies to agonists across plant species. iCB might activate most eudicots' PYL8-like receptors in contrast to opabactin due to reduced steric constraints. This enables iCB to activate prevalent PYL8-like receptors with a bulkier Leu residue in the 3' tunnel, e.g., AtPYL8, SlPYL8, and VviPYL8, whereas opabactin activation is limited to receptors with Val at this position, e.g., TaPYL8. Therefore, iCB extends its action to a broader panel of ABA receptors than CB, iSB09, and opabactin, exhibits higher affinity than ABA for dimeric receptors, and can protect tomato plants against drought. In addition to regulating stomatal conductance and reducing water consumption, iCB protects photosystem II and improves photosynthesis after prolonged water deficit. Moreover, iCB induces an ABA-like transcriptional response, upregulates the synthesis of osmolytes, and can be hyper-potentiated when combined with the expression of a customized receptor. Our results provide structural insight for optimizing agonist design and helping plants cope with water deficit.


  • Organizational Affiliation
    • Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, ES-46022 Valencia, Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Abscisic acid receptor PYL1209Citrus sinensisMutation(s): 0 
Gene Names: CISIN_1g046151mg
UniProt
Find proteins for A0A067E666 (Citrus sinensis)
Explore A0A067E666 
Go to UniProtKB:  A0A067E666
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A067E666
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein phosphatase 2C 16332Arabidopsis thalianaMutation(s): 0 
Gene Names: HAB1P2C-HAAt1g72770F28P22.4
EC: 3.1.3.16
UniProt
Find proteins for Q9CAJ0 (Arabidopsis thaliana)
Explore Q9CAJ0 
Go to UniProtKB:  Q9CAJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CAJ0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IRN (Subject of Investigation/LOI)
Query on A1IRN

Download Ideal Coordinates CCD File 
C [auth A]~{N}-[(4-cyano-3-cyclopropyl-phenyl)methyl]-4-methyl-benzenesulfonamide
C18 H18 N2 O2 S
VUDOMXANWQBNKR-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth B],
E [auth B],
F [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B],
I [auth B],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.213 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.201α = 90
b = 62.736β = 90
c = 187.143γ = 90
Software Package:
Software NamePurpose
autoPROCdata scaling
PHASERphasing
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 UniversitiesSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references