4DS8

Complex structure of abscisic acid receptor PYL3-(+)-ABA-HAB1 in the presence of Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Model: experimental
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Literature

Complex Structures of the Abscisic Acid Receptor PYL3/RCAR13 Reveal a Unique Regulatory Mechanism

Zhang, X.Zhang, Q.Xin, Q.Yu, L.Wang, Z.Wu, W.Jiang, L.Wang, G.Tian, W.Deng, Z.Wang, Y.Liu, Z.Long, J.Gong, Z.Chen, Z.

(2012) Structure 20: 780-790

  • DOI: https://doi.org/10.1016/j.str.2012.02.019
  • Primary Citation of Related Structures:  
    3KL1, 3KLX, 3OJI, 4DS8, 4DSB, 4DSC

  • PubMed Abstract: 

    Abscisic acid (ABA) controls many physiological processes and mediates adaptive responses to abiotic stresses. The ABA signaling mechanisms for abscisic acid receptors PYR/PYL/RCAR (PYLs) were reported. However, it remains unclear whether the molecular mechanisms are suitable for other PYLs. Here, complex structures of PYL3 with (+)-ABA, pyrabactin and HAB1 are reported. An unexpected trans-homodimer intermediate observed in the crystal is confirmed in solution. ABA-bound PYL3 greatly promotes the generation of monomeric PYL3, which can excessively increase the efficiency of inhibiting PP2Cs. Structure-guided biochemical experiments show that Ser195 accounts for the key intermediate. Interestingly, pyrabactin binds to PYL3 in a distinct nonproductive mode with gate closure, which sheds light on the design of agonists and antagonists for abscisic acid receptors. According to different conformations of ligand-bound PYLs, the PYLs family can be divided into three subclasses, among which the trans-dimeric subclass, represented by PYL3, reveals a distinct regulatory mechanism.


  • Organizational Affiliation

    State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Abscisic acid receptor PYL3209Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g73000PYL3
UniProt
Find proteins for Q9SSM7 (Arabidopsis thaliana)
Explore Q9SSM7 
Go to UniProtKB:  Q9SSM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SSM7
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 16343Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g72770HAB1
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.745α = 90
b = 69.723β = 101.63
c = 82.887γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary