9TFY | pdb_00009tfy

Arabidopsis thaliana Casein Kinase 2 (CK2) alpha1 - beta1 complex bound to inositol hexakisphosphate (InsP6)

• PDB DOI: https://doi.org/10.2210/pdb9TFY/pdb

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


• Deposited: 2025-11-27 Released: 2025-12-17 
• Deposition Author(s): Sturm, K., Hothorn, M.
• Funding Organization(s): European Research Council (ERC), Swiss National Science Foundation, Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.50 Å
• R-Value Free: 
  0.267 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: in silico

Literature

An inositol pyrophosphate interaction screen provides insight into the regulation of plant casein kinase II.

Sturm, K., Pri-Tal, O., Rico-Resendiz, F., Verma, Y., Richter, A., Chen, H., Broger, L., Hothorn, L.A., Fiedler, D., Panse, V.G., Hothorn, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 127.37 kDa 
• Atom Count: 8,722 
• Modeled Residue Count: 1,052 
• Deposited Residue Count: 1,076 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha-1	A, B	344	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit beta-1	C, D	194	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CKB1, At5g47080, K14A3.3
UniProt
Find proteins for P40228 (Arabidopsis thaliana) Explore P40228  Go to UniProtKB:  P40228

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	E [auth A], F [auth B]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
ZN	G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.50 Å
• R-Value Free:  0.267 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.189	α = 90
b = 210.189	β = 90
c = 272.599	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Sturm, K., Hothorn, M.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	818696
Swiss National Science Foundation	Switzerland	CRSII5_209412
Howard Hughes Medical Institute (HHMI)	United States	55008733

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release