8AY9

X-RAY CRYSTAL STRUCTURE OF THE CsPYL1(V112L, T135L,F137I, T153I, V168A)-ABA-HAB1 TERNARY COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-guided engineering of a receptor-agonist pair for inducible activation of the ABA adaptive response to drought.

Lozano-Juste, J.Infantes, L.Garcia-Maquilon, I.Ruiz-Partida, R.Merilo, E.Benavente, J.L.Velazquez-Campoy, A.Coego, A.Bono, M.Forment, J.Pampin, B.Destito, P.Monteiro, A.Rodriguez, R.Cruces, J.Rodriguez, P.L.Albert, A.

(2023) Sci Adv 9: eade9948-eade9948

  • DOI: https://doi.org/10.1126/sciadv.ade9948
  • Primary Citation of Related Structures:  
    6ZUC, 8AY3, 8AY6, 8AY7, 8AY8, 8AY9, 8AYA

  • PubMed Abstract: 

    Strategies to activate abscisic acid (ABA) receptors and boost ABA signaling by small molecules that act as ABA receptor agonists are promising biotechnological tools to enhance plant drought tolerance. Protein structures of crop ABA receptors might require modifications to improve recognition of chemical ligands, which in turn can be optimized by structural information. Through structure-based targeted design, we have combined chemical and genetic approaches to generate an ABA receptor agonist molecule (iSB09) and engineer a CsPYL1 ABA receptor, named CsPYL1 5m , which efficiently binds iSB09. This optimized receptor-agonist pair leads to activation of ABA signaling and marked drought tolerance. No constitutive activation of ABA signaling and hence growth penalty was observed in transformed Arabidopsis thaliana plants. Therefore, conditional and efficient activation of ABA signaling was achieved through a chemical-genetic orthogonal approach based on iterative cycles of ligand and receptor optimization driven by the structure of ternary receptor-ligand-phosphatase complexes.


  • Organizational Affiliation

    Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 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): 5 
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 16333Arabidopsis 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A8S (Subject of Investigation/LOI)
Query on A8S

Download Ideal Coordinates CCD File 
C [auth A](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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
N [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.763α = 90
b = 62.923β = 90
c = 187.01γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIXrefinement

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 UniversitiesSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-02-28
    Changes: Structure summary