4JDA | pdb_00004jda

Complex structure of abscisic acid receptor PYL3 with (-)-ABA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.267 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

Starting Model: experimental
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Literature

Structural Insights into the Abscisic Acid Stereospecificity by the ABA Receptors PYR/PYL/RCAR

Zhang, X.Jiang, L.Wang, G.Yu, L.Zhang, Q.Xin, Q.Wu, W.Gong, Z.Chen, Z.

(2013) PLoS One 8: e67477-e67477

  • DOI: https://doi.org/10.1371/journal.pone.0067477
  • Primary Citation Related Structures: 
    3OQU, 4JDA, 4JDL

  • PubMed Abstract: 

    The phytohormone abscisic acid ((+)-ABA) plays a key role in many processes. The biological and biochemical activities of unnatural (-)-ABA have been extensively investigated since 1960s. However, the recognition mechanism by which only a few members among PYR/PYL/RCAR (PYLs) family can bind (-)-ABA remains largely unknown. Here we systematically characterized the affinity of PYLs binding to the (-)-ABA and reported the crystal structures of apo-PYL5, PYL3-(-)-ABA and PYL9-(+)-ABA. PYL5 showed the strongest binding affinity with (-)-ABA among all the PYLs. PYL9 is a stringently exclusive (+)-ABA receptor with interchangeable disulfide bonds shared by a subclass of PYLs. PYL3 is a dual receptor to both ABA enantiomers. The binding orientation and pocket of (-)-ABA in PYLs are obviously different from those of (+)-ABA. Steric hindrance and hydrophobic interaction are the two key factors in determining the stereospecificity of PYLs binding to (-)-ABA, which is further confirmed by gain-of-function and loss-of-function mutagenesis. Our results provide novel insights of the bioactivity of ABA enantiomers onto PYLs, and shed light on designing the selective ABA receptors agonists.


  • Organizational Affiliation
    • State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 87.64 kDa 
  • Atom Count: 5,396 
  • Modeled Residue Count: 695 
  • Deposited Residue Count: 768 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Abscisic acid receptor PYL3
A, B, C, D
192Arabidopsis thalianaMutation(s): 0 
Gene Names: PYL3
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.267 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.738α = 90
b = 142.738β = 90
c = 99.802γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description