3WG8 | pdb_00003wg8

Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist AS6

• PDB DOI: https://doi.org/10.2210/pdb3WG8/pdb

• Classification: HORMONE RECEPTOR
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-31 Released: 2014-05-07 
• Deposition Author(s): Akiyama, T., Sue, M., Takeuchi, J., Okamoto, M., Muto, T., Endo, A., Nambara, E., Hirai, N., Ohnishi, T., Cutler, S.R., Todoroki, Y., Yajima, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.281 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.237 (Depositor) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Designed abscisic acid analogs as antagonists of PYL-PP2C receptor interactions

Takeuchi, J., Okamoto, M., Akiyama, T., Muto, T., Yajima, S., Sue, M., Seo, M., Kanno, Y., Kamo, T., Endo, A., Nambara, E., Hirai, N., Ohnishi, T., Cutler, S.R., Todoroki, Y.

(2014) Nat Chem Biol 10: 477-482

• PubMed: 24792952 
• DOI: https://doi.org/10.1038/nchembio.1524
• Primary Citation Related Structures: 
  3WG8


• PubMed Abstract: 
  

  The plant stress hormone abscisic acid (ABA) is critical for several abiotic stress responses. ABA signaling is normally repressed by group-A protein phosphatases 2C (PP2Cs), but stress-induced ABA binds Arabidopsis PYR/PYL/RCAR (PYL) receptors, which then bind and inhibit PP2Cs. X-ray structures of several receptor-ABA complexes revealed a tunnel above ABA's 3' ring CH that opens at the PP2C binding interface. Here, ABA analogs with sufficiently long 3' alkyl chains were predicted to traverse this tunnel and block PYL-PP2C interactions. To test this, a series of 3'-alkylsulfanyl ABAs were synthesized with different alkyl chain lengths. Physiological, biochemical and structural analyses revealed that a six-carbon alkyl substitution produced a potent ABA antagonist that was sufficiently active to block multiple stress-induced ABA responses in vivo. This study provides a new approach for the design of ABA analogs, and the results validated structure-based design for this target class.

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Organizational Affiliation: 
• 1] Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan. [2].
1] Arid Land Research Center, Tottori University, Tottori, Japan. [2] Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California-Riverside, Riverside, California, USA. [3].
Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan.
Graduate School of Agriculture, Shizuoka University, Shizuoka, Japan.
Department of Applied Biology and Chemistry, Tokyo University of Agriculture, Tokyo, Japan.
RIKEN Center for Sustainable Resource Science, Kanagawa, Japan.
National Institute for Agro-Environmental Sciences, Ibaraki, Japan.
1] Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada. [2].
Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.
Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
1] Graduate School of Agriculture, Shizuoka University, Shizuoka, Japan. [2] Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan.
Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California-Riverside, Riverside, California, USA.
1] Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan. [2] Graduate School of Agriculture, Shizuoka University, Shizuoka, Japan. [3] Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.81 kDa 
• Atom Count: 1,467 
• Modeled Residue Count: 175 
• Deposited Residue Count: 227 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Abscisic acid receptor PYR1	A	227	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PYR1
UniProt
Find proteins for O49686 (Arabidopsis thaliana) Explore O49686  Go to UniProtKB:  O49686

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6AS	B [auth A]	(2Z,4E)-5-[(1S)-3-(hexylsulfanyl)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid C21 H32 O4 S AOFXVHRNNSAVEA-IHZHKDPYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.281 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.237 (Depositor) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.932	α = 90
b = 66.932	β = 90
c = 78.237	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-07 
Deposition Author(s): Akiyama, T., Sue, M., Takeuchi, J., Okamoto, M., Muto, T., Endo, A., Nambara, E., Hirai, N., Ohnishi, T., Cutler, S.R., Todoroki, Y., Yajima, S.

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2014-06-11
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description