3KLX | pdb_00003klx

Crystal structure of native abscisic acid receptor PYL3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.270 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.252 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 
    0.253 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3KLX

This is version 1.3 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 46.84 kDa 
  • Atom Count: 2,883 
  • Modeled Residue Count: 361 
  • Deposited Residue Count: 418 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
F3N23.20 protein
A, B
209Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g73000F3N23.20pyl3
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: 2.50 Å
  • R-Value Free:  0.270 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.252 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.964α = 90
b = 86.964β = 90
c = 154.118γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-06-06
    Changes: Database references
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations