3NJO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.473 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nsmb.1898
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Abscisic acid receptor PYR1
A, B, C
194Arabidopsis thalianaMutation(s): 1 
Gene Names: PYR1 (ABIP6, RCAR11)
Find proteins for O49686 (Arabidopsis thaliana)
Go to UniProtKB:  O49686
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P2M
Query on P2M

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Download CCD File 
B
N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide
C16 H14 N2 O2 S
LYUIYUXDRYTIOE-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PYV
Query on PYV

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Download CCD File 
A, C
4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide
Pyrabactin
C16 H13 Br N2 O2 S
GJSDYQXOSHKOGX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.473 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 60.307α = 90.00
b = 60.307β = 90.00
c = 527.599γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
PHENIXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Advisory, Refinement description