6NWC

PYL10 bound to the ABA pan-agonist 3CB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Dynamic control of plant water use using designed ABA receptor agonists.

Vaidya, A.S.Helander, J.D.M.Peterson, F.C.Elzinga, D.Dejonghe, W.Kaundal, A.Park, S.Y.Xing, Z.Mega, R.Takeuchi, J.Khanderahoo, B.Bishay, S.Volkman, B.F.Todoroki, Y.Okamoto, M.Cutler, S.R.

(2019) Science 366

  • DOI: https://doi.org/10.1126/science.aaw8848
  • Primary Citation of Related Structures:  
    6NWC

  • PubMed Abstract: 

    Drought causes crop losses worldwide, and its impact is expected to increase as the world warms. This has motivated the development of small-molecule tools for mitigating the effects of drought on agriculture. We show here that current leads are limited by poor bioactivity in wheat, a widely grown staple crop, and in tomato. To address this limitation, we combined virtual screening, x-ray crystallography, and structure-guided design to develop opabactin (OP), an abscisic acid (ABA) mimic with up to an approximately sevenfold increase in receptor affinity relative to ABA and up to 10-fold greater activity in vivo. Studies in Arabidopsis thaliana reveal a role of the type III receptor PYRABACTIN RESISTANCE-LIKE 2 for the antitranspirant efficacy of OP. Thus, virtual screening and structure-guided optimization yielded newly discovered agonists for manipulating crop abiotic stress tolerance and water use.


  • Organizational Affiliation

    Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Abscisic acid receptor PYL10155Arabidopsis thalianaMutation(s): 0 
Gene Names: PYL10RCAR4At4g27920T13J8.30
UniProt
Find proteins for Q8H1R0 (Arabidopsis thaliana)
Explore Q8H1R0 
Go to UniProtKB:  Q8H1R0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8H1R0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L6P
Query on L6P

Download Ideal Coordinates CCD File 
B [auth A]1-{[(4-cyano-3-cyclopropylphenyl)acetyl]amino}cyclohexane-1-carboxylic acid
C19 H22 N2 O3
XZXSSWDGVSHUNZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.63α = 90
b = 67.63β = 90
c = 63.776γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States12581750
National Science Foundation (NSF, United States)United States165689

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description