3W9R

Crystal structure of the high-affinity abscisic acid receptor PYL9/RCAR9 bound to ABA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mechanism of high-affinity abscisic acid binding to PYL9/RCAR1.

Nakagawa, M.Kagiyama, M.Shibata, N.Hirano, Y.Hakoshima, T.

(2014) Genes Cells 19: 386-404

  • DOI: https://doi.org/10.1111/gtc.12140
  • Primary Citation of Related Structures:  
    3W9R

  • PubMed Abstract: 

    Arabidopsis receptors of abscisic acid (ABA), the key plant hormone for adaptation to water stress, comprise 14 PYR/PYLs/RCARs proteins classified into three subfamilies I, II, and III, which suggests functional differentiation. Although their monomer-dimer equilibria may be correlated with differences in their ABA-binding affinities, how the dimerization decreases the affinity is unclear. Comparative structural and binding studies between PYL9, which is a representative of high-affinity subfamily I, and low-affinity members of subfamily III reveals that the nonpolar triplet (Ile110, Val162, and Leu165) and Pro64 contribute to enhance ABA-binding affinity by inducing a shift of the ABA carboxyl group to form additional direct hydrogen bonds with conserved Asn169. Our mutation studies of PYL1 successfully produced a monomeric mutant PYL1 exhibiting low ABA affinity and also a dimeric mutant PYL1 exhibiting high ABA-binding affinity, suggesting that dimer formation of ABA receptors is not essential for their low ABA-binding affinity. Our study contributes toward establishing the structural basis for the higher ABA-binding affinity of the subfamily receptors and provides a clue for understanding the broad spectrum of hormone actions in plants manifested by the different hormone-binding affinity of multiple receptors.


  • Organizational Affiliation

    Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Abscisic acid receptor PYL9189Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g01360F6F3.16PYL9RCAR1
UniProt
Find proteins for Q84MC7 (Arabidopsis thaliana)
Explore Q84MC7 
Go to UniProtKB:  Q84MC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84MC7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download Ideal Coordinates CCD File 
C [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
A8S
Query on A8S

Download Ideal Coordinates CCD File 
B [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
Binding Affinity Annotations 
IDSourceBinding Affinity
A8S Binding MOAD:  3W9R Kd: 660 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.405α = 90
b = 111.405β = 90
c = 40.478γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Refinement description