3K3K | pdb_00003k3k

Crystal structure of dimeric abscisic acid (ABA) receptor pyrabactin resistance 1 (PYR1) with ABA-bound closed-lid and ABA-free open-lid subunits

• PDB DOI: https://doi.org/10.2210/pdb3K3K/pdb

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


• Deposited: 2009-10-02 Released: 2009-11-17 
• Deposition Author(s): Arvai, A.S., Hitomi, K., Getzoff, E.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.237 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structural mechanism of abscisic acid binding and signaling by dimeric PYR1.

Nishimura, N., Hitomi, K., Arvai, A.S., Rambo, R.P., Hitomi, C., Cutler, S.R., Schroeder, J.I., Getzoff, E.D.

(2009) Science 326: 1373-1379

• PubMed: 19933100 
• DOI: https://doi.org/10.1126/science.1181829
• Primary Citation Related Structures: 
  3K3K


• PubMed Abstract: 
  

  The phytohormone abscisic acid (ABA) acts in seed dormancy, plant development, drought tolerance, and adaptive responses to environmental stresses. Structural mechanisms mediating ABA receptor recognition and signaling remain unknown but are essential for understanding and manipulating abiotic stress resistance. Here, we report structures of pyrabactin resistance 1 (PYR1), a prototypical PYR/PYR1-like (PYL)/regulatory component of ABA receptor (RCAR) protein that functions in early ABA signaling. The crystallographic structure reveals an alpha/beta helix-grip fold and homodimeric assembly, verified in vivo by coimmunoprecipitation. ABA binding within a large internal cavity switches structural motifs distinguishing ABA-free "open-lid" from ABA-bound "closed-lid" conformations. Small-angle x-ray scattering suggests that ABA signals by converting PYR1 to a more compact, symmetric closed-lid dimer. Site-directed PYR1 mutants designed to disrupt hormone binding lose ABA-triggered interactions with type 2C protein phosphatase partners in planta.

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Organizational Affiliation: 
• Division of Biological Sciences, Cell and Developmental Biology Section, University of California at San Diego, La Jolla, CA 92093, USA.

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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.81 kDa 
• Atom Count: 3,438 
• Modeled Residue Count: 366 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Abscisic acid receptor PYR1	A, B	211	Arabidopsis thaliana	Mutation(s): 0  Gene Names: AT4g17870, PYR1, T6K21.50
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
A8S	C [auth B]	(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.237 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.208	α = 90
b = 61.407	β = 98.97
c = 82.844	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Arvai, A.S., Hitomi, K., Getzoff, E.D.

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary