9TB5 | pdb_00009tb5

Crystal structure of the MpPYL1-ABA-HAB1 ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.291 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Evolutionary-based remodeling of ABA receptors reveals the structural basis of hormone perception and regulation.

Rivera-Moreno, M.Bono, M.Infantes, L.Rodriguez, P.L.Albert, A.

(2026) Proc Natl Acad Sci U S A 123: e2534140123-e2534140123

  • DOI: https://doi.org/10.1073/pnas.2534140123
  • Primary Citation Related Structures: 
    9TB5, 9TB6, 9TB7, 9TB8, 9TB9, 9TBA, 9TBB, 9TBC

  • PubMed Abstract: 

    Drought limits crop productivity, and effective mitigation requires a mechanistic understanding of how abscisic acid (ABA) perception translates hormone levels into physiological responses. In seed plants, ABA is sensed by PYR/PYL/RCAR (PYR/PYL) receptors, which inhibit 2C protein phosphatases (PP2Cs), thereby releasing Snf1-related protein kinases and driving stomatal closure and stress-responsive transcription. Yet how receptor architecture evolved to tune ABA dependence and dynamic range remains unclear. Here, we combine structural biology, biochemistry, evolutionary analysis, and in planta assays across algal, bryophyte, and angiosperm receptors to uncover a minimal molecular code that governs ABA sensitivity and oligomeric state. We identify a five-residue signature: Three leucines in the ligand pocket stabilize the gate in a closed conformation, conferring ligand-independent PP2C inhibition (ancestral trait), while two interface residues toggle dimerization (Leu/Lys) versus monomerization (Cys/Ser), thereby setting ABA affinity. Structure-guided swaps reciprocally convert behaviors: Introducing the three leucines plus interface substitutions renders the ABA-dependent dimeric Citrus sinensis CsPYL1 into a monomer-like with ABA-independent activity, whereas the converse changes in monomeric Marchantia polymorpha MpPYL1 enforce dimerization and lower ABA affinity. In planta, reporter assays and mutant analyses reveal complementary operating ranges: Monomeric, high-affinity receptors decode low ABA under mild stress, while dimeric, reduced-affinity receptors sustain signaling at high ABA during acute drought, expanding the system's overall dynamic range and robustness. These results resolve the apparent paradox of low-affinity dimers as an evolutionary innovation rather than a loss of sensitivity, link receptor architecture to ABA-mediated response, and provide actionable design principles for engineering ABA signaling to enhance crop drought resilience.


  • Organizational Affiliation
    • Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid ES-28006, Spain.

Macromolecule Content 

  • Total Structure Weight: 58.87 kDa 
  • Atom Count: 4,008 
  • Modeled Residue Count: 506 
  • Deposited Residue Count: 523 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MpPYL1 receptor190Marchantia polymorphaMutation(s): 0 
Gene Names: MARPO_0030s0080
UniProt
Find proteins for A0A2R6X8C9 (Marchantia polymorpha)
Explore A0A2R6X8C9 
Go to UniProtKB:  A0A2R6X8C9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2R6X8C9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.291 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.06α = 90
b = 71.997β = 90
c = 103.546γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata 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 UniversitiesSpainPID2023-153108OB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-06
    Type: Initial release