3NJO | pdb_00003njo

X-ray crystal structure of the Pyr1-pyrabactin A complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 
    0.265 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural basis for selective activation of ABA receptors.

Peterson, F.C.Burgie, E.S.Park, S.Y.Jensen, D.R.Weiner, J.J.Bingman, C.A.Chang, C.E.Cutler, S.R.Phillips, G.N.Volkman, B.F.

(2010) Nat Struct Mol Biol 17: 1109-1113

  • DOI: https://doi.org/10.1038/nsmb.1898
  • Primary Citation Related Structures: 
    3NJ0, 3NJ1, 3NJO

  • PubMed Abstract: 

    Changing environmental conditions and lessening fresh water supplies have sparked intense interest in understanding and manipulating abscisic acid (ABA) signaling, which controls adaptive responses to drought and other abiotic stressors. We recently discovered a selective ABA agonist, pyrabactin, and used it to discover its primary target PYR1, the founding member of the PYR/PYL family of soluble ABA receptors. To understand pyrabactin's selectivity, we have taken a combined structural, chemical and genetic approach. We show that subtle differences between receptor binding pockets control ligand orientation between productive and nonproductive modes. Nonproductive binding occurs without gate closure and prevents receptor activation. Observations in solution show that these orientations are in rapid equilibrium that can be shifted by mutations to control maximal agonist activity. Our results provide a robust framework for the design of new agonists and reveal a new mechanism for agonist selectivity.


  • Organizational Affiliation
    • Department of Biochemistry and Center for Eukaryotic Structural Genomics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.

Macromolecule Content 

  • Total Structure Weight: 66.93 kDa 
  • Atom Count: 4,368 
  • Modeled Residue Count: 517 
  • Deposited Residue Count: 582 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Abscisic acid receptor PYR1
A, B, C
194Arabidopsis thalianaMutation(s): 1 
Gene Names: ABIP6At4g17870PYR1RCAR11T6K21.50
UniProt
Find proteins for O49686 (Arabidopsis thaliana)
Explore O49686 
Go to UniProtKB:  O49686
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO49686
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PYV

Query on PYV



Download:Ideal Coordinates CCD File
D [auth A],
I [auth C]
4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide
C16 H13 Br N2 O2 S
GJSDYQXOSHKOGX-UHFFFAOYSA-N
P2M

Query on P2M



Download:Ideal Coordinates CCD File
G [auth B]N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide
C16 H14 N2 O2 S
LYUIYUXDRYTIOE-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
J [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free:  0.265 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.307α = 90
b = 60.307β = 90
c = 527.599γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.3: 2021-10-06
    Changes: Advisory, Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description