9J6I | pdb_00009j6i

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

• PDB DOI: https://doi.org/10.2210/pdb9J6I/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-08-16 Released: 2024-09-04 
• Deposition Author(s): Yan, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.252 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

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

• PubMed: 39277642 
• DOI: https://doi.org/10.1038/s41467-024-52426-y
• Primary Citation 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.

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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.
Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China.
State Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China.
State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang, 550025, China.
State Key Laboratory of Tree Genetics and Breeding, the Southern Modern Forestry Collaborative Innovation Center, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, 271018, China.
Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China. [e-mail].
State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China. [e-mail].
State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang, 550025, China. [e-mail].
State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.04 kDa 
• Atom Count: 2,784 
• Modeled Residue Count: 338 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Abscisic acid receptor PYL1	A, B	175	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PYL1, RCAR12, At5g46790, MZA15.21
UniProt
Find proteins for Q8VZS8 (Arabidopsis thaliana) Explore Q8VZS8  Go to UniProtKB:  Q8VZS8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H9X (Subject of Investigation/LOI)	C [auth B]	4-bromo-N-[(4-bromophenyl)di(hydroxy)-lambda~4~-sulfanyl]-2,6-dinitroaniline C12 H9 Br2 N3 O6 S VADPHRCUIKWCQV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.252 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.99	α = 90
b = 126.99	β = 90
c = 60.195	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Database references, Structure summary
• Version 2.0: 2026-04-15
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary