4PSB | pdb_00004psb

Crystal Structure of Phytohormone Binding Protein from Vigna radiata in complex with gibberellic acid (GA3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.204 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Specific binding of gibberellic acid by Cytokinin-Specific Binding Proteins: a new aspect of plant hormone-binding proteins with the PR-10 fold.

Ruszkowski, M.Sliwiak, J.Ciesielska, A.Barciszewski, J.Sikorski, M.Jaskolski, M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2032-2041

  • DOI: https://doi.org/10.1107/S1399004714010578
  • Primary Citation Related Structures: 
    4PSB, 4Q0K

  • PubMed Abstract: 

    Pathogenesis-related proteins of class 10 (PR-10) are a family of plant proteins with the same fold characterized by a large hydrophobic cavity that allows them to bind various ligands, such as phytohormones. A subfamily with only ~20% sequence identity but with a conserved canonical PR-10 fold have previously been recognized as Cytokinin-Specific Binding Proteins (CSBPs), although structurally the binding mode of trans-zeatin (a cytokinin phytohormone) was found to be quite diversified. Here, it is shown that two CSBP orthologues from Medicago truncatula and Vigna radiata bind gibberellic acid (GA3), which is an entirely different phytohormone, in a conserved and highly specific manner. In both cases a single GA3 molecule is found in the internal cavity of the protein. The structural data derived from high-resolution crystal structures are corroborated by isothermal titration calorimetry (ITC), which reveals a much stronger interaction with GA3 than with trans-zeatin and pH dependence of the binding profile. As a conclusion, it is postulated that the CSBP subfamily of plant PR-10 proteins should be more properly linked with general phytohormone-binding properties and termed phytohormone-binding proteins (PhBP).


  • Organizational Affiliation
    • Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.

Macromolecule Content 

  • Total Structure Weight: 17.96 kDa 
  • Atom Count: 1,436 
  • Modeled Residue Count: 152 
  • Deposited Residue Count: 155 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytokinin-specific binding protein155Vigna radiataMutation(s): 0 
Gene Names: vrphbp
UniProt
Find proteins for A0A1S3THR8 (Vigna radiata var. radiata)
Explore A0A1S3THR8 
Go to UniProtKB:  A0A1S3THR8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3THR8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GA3

Query on GA3



Download:Ideal Coordinates CCD File
B [auth A]GIBBERELLIN A3
C19 H22 O6
IXORZMNAPKEEDV-OBDJNFEBSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.204 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.38α = 90
b = 54.29β = 98.7
c = 71.09γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Data collection
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary