Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 57.84 kDa 
• Atom Count: 3701 
• Modelled Residue Count: 457 
• Deposited Residue Count: 507 
• Unique protein chains: 1

3KU2

Crystal Structure of inactivated form of CDPK1 from toxoplasma gondii, TGME49.101440

• DOI: 10.2210/pdb3KU2/pdb

• Classification: TRANSFERASE
• Organism(s): Toxoplasma gondii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-26 Released: 2010-02-16 
• Deposition Author(s): Wernimont, A.K., Artz, J.D., Finnerty, P., Xiao, T., He, H., Mackenzie, F., Sinestera, G., Hassani, A.A., Wasney, G., Vedadi, M., Lourido, S., Bochkarev, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Sibley, D.L., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 

Literature

Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium.

Wernimont, A.K., Artz, J.D., Finerty, P., Lin, Y.H., Amani, M., Allali-Hassani, A., Senisterra, G., Vedadi, M., Tempel, W., Mackenzie, F., Chau, I., Lourido, S., Sibley, L.D., Hui, R.

(2010) Nat Struct Mol Biol 17: 596-601

• PubMed: 20436473 
• DOI: 10.1038/nsmb.1795
• Primary Citation of Related Structures:  
  3KU2, 3HX4, 3HZT, 3IGO


• PubMed Abstract: 
  

Calcium-dependent protein kinases (CDPKs) have pivotal roles in the calcium-signaling pathway in plants, ciliates and apicomplexan parasites and comprise a calmodulin-dependent kinase (CaMK)-like kinase domain regulated by a calcium-binding domain in the C terminus. To understand this intramolecular mechanism of activation, we solved the structures of the autoinhibited (apo) and activated (calcium-bound) conformations of CDPKs from the apicomplexan parasites Toxoplasma gondii and Cryptosporidium parvum. In the apo form, the C-terminal CDPK activation domain (CAD) resembles a calmodulin protein with an unexpected long helix in the N terminus that inhibits the kinase domain in the same manner as CaMKII. Calcium binding triggers the reorganization of the CAD into a highly intricate fold, leading to its relocation around the base of the kinase domain to a site remote from the substrate binding site. This large conformational change constitutes a distinct mechanism in calcium signal-transduction pathways.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-domain protein kinase 1	A	507	Toxoplasma gondii	Mutation(s): 0  Gene Names: CDPK1, TGME49_101440
UniProt
Find proteins for Q9BJF5 (Toxoplasma gondii) Explore Q9BJF5  Go to UniProtKB:  Q9BJF5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
UNX	C [auth A], D [auth A], E [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.01	α = 90
b = 72.912	β = 96.26
c = 65.018	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
DENZO	data reduction

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2009-11-26 
• Released Date: 2010-02-16 
Deposition Author(s): Wernimont, A.K., Artz, J.D., Finnerty, P., Xiao, T., He, H., Mackenzie, F., Sinestera, G., Hassani, A.A., Wasney, G., Vedadi, M., Lourido, S., Bochkarev, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Sibley, D.L., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2019-07-17
  Changes: Data collection, Refinement description