6XX6

Arabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal form I

• PDB DOI: https://doi.org/10.2210/pdb6XX6/pdb

• Classification: CELL CYCLE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-01-27 Released: 2020-04-15 
• Deposition Author(s): Demulder, M., De Veylder, L., Loris, R.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.199 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

Crystal structure of Arabidopsis thaliana casein kinase 2 alpha 1.

Demulder, M., De Veylder, L., Loris, R.

(2020) Acta Crystallogr F Struct Biol Commun 76: 182-191

• PubMed: 32254052 
• DOI: https://doi.org/10.1107/S2053230X20004537
• Primary Citation of Related Structures:  
  6XX6, 6XX7, 6XX8, 6XX9


• PubMed Abstract: 
  

  Casein kinase 2 (CK2) is a ubiquitous pleiotropic enzyme that is highly conserved across eukaryotic kingdoms. CK2 is singular amongst kinases as it is highly rigid and constitutively active. Arabidopsis thaliana is widely used as a model system in molecular plant research; the biological functions of A. thaliana CK2 are well studied in vivo and many of its substrates have been identified. Here, crystal structures of the α subunit of A. thaliana CK2 in three crystal forms and of its complex with the nonhydrolyzable ATP analog AMppNHp are presented. While the C-lobe of the enzyme is highly rigid, structural plasticity is observed for the N-lobe. Small but significant displacements within the active cleft are necessary in order to avoid steric clashes with the AMppNHp molecule. Binding of AMppNHp is influenced by a rigid-body motion of the N-lobe that was not previously recognized in maize CK2.

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Organizational Affiliation: 

Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.94 kDa 
• Atom Count: 3,168 
• Modelled Residue Count: 330 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha-1	A	342	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CKA1, At5g67380, K8K14.10 EC: 2.7.11.1
UniProt
Find proteins for Q08467 (Arabidopsis thaliana) Explore Q08467  Go to UniProtKB:  Q08467

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	F [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PIV	B [auth A]	PIVALIC ACID C5 H10 O2 IUGYQRQAERSCNH-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.199 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.98	α = 90
b = 61.98	β = 90
c = 227.73	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Demulder, M., De Veylder, L., Loris, R.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G023616N
Research Foundation - Flanders (FWO)	Belgium	G011420N

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description