9J6I | pdb_00009j6i

Crystal structure of the ABA receptor PYL1 in complex with DBSA compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.252 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Stabilization of dimeric PYR/PYL/RCAR family members relieves abscisic acid-induced inhibition of seed germination.

Wang, Z.Z.Cao, M.J.Yan, J.Dong, J.Chen, M.X.Yang, J.F.Li, J.H.Ying, R.N.Gao, Y.Y.Li, L.Leng, Y.N.Tian, Y.Hewage, K.A.H.Pei, R.J.Huang, Z.Y.Yin, P.Zhu, J.K.Hao, G.F.Yang, G.F.

(2024) Nat Commun 15: 8077-8077

  • DOI: https://doi.org/10.1038/s41467-024-52426-y
  • Primary Citation of Related Structures:  
    9J6I

  • PubMed Abstract: 

    Abscisic acid (ABA) is the primary preventing factor of seed germination, which is crucial to plant survival and propagation. ABA-induced seed germination inhibition is mainly mediated by the dimeric PYR/PYL/RCAR (PYLs) family members. However, little is known about the relevance between dimeric stability of PYLs and seed germination. Here, we reveal that stabilization of PYL dimer can relieve ABA-induced inhibition of seed germination using chemical genetic approaches. Di-nitrobensulfamide (DBSA), a computationally designed chemical probe, yields around ten-fold improvement in receptor affinity relative to ABA. DBSA reverses ABA-induced inhibition of seed germination mainly through dimeric receptors and recovers the expression of ABA-responsive genes. DBSA maintains PYR1 in dimeric state during protein oligomeric state experiment. X-ray crystallography shows that DBSA targets a pocket in PYL dimer interface and may stabilize PYL dimer by forming hydrogen networks. Our results illustrate the potential of PYL dimer stabilization in preventing ABA-induced seed germination inhibition.


  • Organizational Affiliation

    State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Abscisic acid receptor PYL1
A, B
175Arabidopsis thalianaMutation(s): 0 
Gene Names: PYL1RCAR12At5g46790MZA15.21
UniProt
Find proteins for Q8VZS8 (Arabidopsis thaliana)
Explore Q8VZS8 
Go to UniProtKB:  Q8VZS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VZS8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H9X (Subject of Investigation/LOI)
Query on H9X

Download Ideal Coordinates CCD File 
C [auth B]5-bromanyl-N2-[(4-bromophenyl)-bis(oxidanyl)-$l^4-sulfanyl]-N1,N1,N3,N3-tetrakis(oxidanyl)benzene-1,2,3-triamine
C12 H13 Br2 N3 O6 S
NHTMTRVPPRZTCB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.252 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.99α = 90
b = 126.99β = 90
c = 60.195γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted H9XClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2024-09-04 
  • Deposition Author(s): Yan, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary