9TFW | pdb_00009tfw

Arabidopsis thaliana Casein Kinase 2 (CK2) alpha isoform 3 apo

• PDB DOI: https://doi.org/10.2210/pdb9TFW/pdb

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


• Deposited: 2025-11-27 Released: 2025-12-24 
• 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: 1.25 Å
• R-Value Free: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.61 kDa 
• Atom Count: 3,177 
• Modeled Residue Count: 335 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha-3	A	341	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CKA3, At2g23080, F21P24.14 EC: 2.7.11.1
UniProt
Find proteins for O64817 (Arabidopsis thaliana) Explore O64817  Go to UniProtKB:  O64817

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEZ	B [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.979	α = 90
b = 59.556	β = 90
c = 107.013	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
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: 2025-12-24
  Type: Initial release