3NEF | pdb_00003nef

High-resolution pyrabactin-bound PYL1 structure

• PDB DOI: https://doi.org/10.2210/pdb3NEF/pdb

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


• Deposited: 2010-06-08 Released: 2010-06-16 
• Deposition Author(s): Yan, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Functional mechanism of the ABA agonist pyrabactin

Hao, Q., Yin, P., Yan, C., Yuan, X., Li, W., Zhang, Z., Liu, L., Wang, J., Yan, N.

(2010) J Biological Chem 285: 28946-28952

• PubMed: 20554531 
• DOI: https://doi.org/10.1074/jbc.M110.149005
• Primary Citation Related Structures: 
  3NEF, 3NEG


• PubMed Abstract: 
  

  Pyrabactin is a synthetic abscisic acid (ABA) agonist that selectively inhibits seed germination. The use of pyrabactin was pivotal in the identification of the PYR1/PYL/RCAR family (PYL) of proteins as the ABA receptor. Although they both act through PYL proteins, pyrabactin and ABA share no apparent chemical or structural similarity. It remains unclear how pyrabactin functions as an ABA agonist. Here, we report the crystal structure of pyrabactin in complex with PYL1 at 2.4 A resolution. Structural and biochemical analyses revealed that recognition of pyrabactin by the pocket residues precedes the closure of switch loop CL2. Structural comparison between pyrabactin- and ABA-bound PYL1 reveals a general principle in the arrangements of function groups of the two distinct ligands. The study provides a framework for the development of novel ABA agonists that may have applicable potentials in agriculture.

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Organizational Affiliation: 
• State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.03 kDa 
• Atom Count: 3,015 
• Modeled Residue Count: 359 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Abscisic acid receptor PYL1	A, B	202	Arabidopsis thaliana	Mutation(s): 0  EC: 3.1.3.16
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
PYV	C [auth A]	4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide C16 H13 Br N2 O2 S GJSDYQXOSHKOGX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.57	α = 90
b = 128.57	β = 90
c = 87.24	γ = 120

Software Package:

Software Name	Purpose
BSS	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-16 
Deposition Author(s): Yan, N.

Revision History  

• Version 1.0: 2010-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description