6Z1C

Crystal structure of Arabidopsis thaliana CK2-alpha-1 in complex with TTP-22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Arabidopsis casein kinase 2 triggers stem cell exhaustion under Al toxicity and phosphate deficiency through activating the DNA damage response pathway.

Wei, P.Demulder, M.David, P.Eekhout, T.Yoshiyama, K.O.Nguyen, L.Vercauteren, I.Eeckhout, D.Galle, M.De Jaeger, G.Larsen, P.Audenaert, D.Desnos, T.Nussaume, L.Loris, R.De Veylder, L.

(2021) Plant Cell 33: 1361-1380

  • DOI: https://doi.org/10.1093/plcell/koab005
  • Primary Citation of Related Structures:  
    6Z1C

  • PubMed Abstract: 

    Aluminum (Al) toxicity and inorganic phosphate (Pi) limitation are widespread chronic abiotic and mutually enhancing stresses that profoundly affect crop yield. Both stresses strongly inhibit root growth, resulting from a progressive exhaustion of the stem cell niche. Here, we report on a casein kinase 2 (CK2) inhibitor identified by its capability to maintain a functional root stem cell niche in Arabidopsis thaliana under Al toxic conditions. CK2 operates through phosphorylation of the cell cycle checkpoint activator SUPPRESSOR OF GAMMA RADIATION1 (SOG1), priming its activity under DNA-damaging conditions. In addition to yielding Al tolerance, CK2 and SOG1 inactivation prevents meristem exhaustion under Pi starvation, revealing the existence of a low Pi-induced cell cycle checkpoint that depends on the DNA damage activator ATAXIA-TELANGIECTASIA MUTATED (ATM). Overall, our data reveal an important physiological role for the plant DNA damage response pathway under agriculturally limiting growth conditions, opening new avenues to cope with Pi limitation.


  • Organizational Affiliation

    Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha-1333Arabidopsis thalianaMutation(s): 0 
Gene Names: CKA1At5g67380K8K14.10
EC: 2.7.11.1
UniProt
Find proteins for Q08467 (Arabidopsis thaliana)
Explore Q08467 
Go to UniProtKB:  Q08467
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08467
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.25α = 90
b = 81.11β = 108.64
c = 48.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2021-06-09
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description