3IGO | pdb_00003igo

Crystal structure of Cryptosporidium parvum CDPK1, cgd3_920

• PDB DOI: https://doi.org/10.2210/pdb3IGO/pdb

• Classification: TRANSFERASE
• Organism(s): Cryptosporidium parvum Iowa II
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-28 Released: 2009-08-11 
• Deposition Author(s): Wernimont, A.K., Artz, J.D., Finnerty, P., Amani, M., Allali-Hassanali, A., Vedadi, M., Tempel, W., MacKenzie, F., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Bochkarev, A., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.258 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1038/nsmb.1795
• Primary Citation Related Structures: 
  3HX4, 3HZT, 3IGO, 3KU2


• 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.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.62 kDa 
• Atom Count: 3,761 
• Modeled Residue Count: 446 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-domain protein kinase 1	A	486	Cryptosporidium parvum Iowa II	Mutation(s): 0  Gene Names: cgd3_920 EC: 2.7.11.1
UniProt
Find proteins for A3FQ16 (Cryptosporidium parvum (strain Iowa II)) Explore A3FQ16  Go to UniProtKB:  A3FQ16

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	E [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SRT	K [auth A]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
PO4	M [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A], G [auth A], H [auth A], J [auth A], L [auth A], N [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.258 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.388	α = 90
b = 55.55	β = 105.25
c = 81.697	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-11 
Deposition Author(s): Wernimont, A.K., Artz, J.D., Finnerty, P., Amani, M., Allali-Hassanali, A., Vedadi, M., Tempel, W., MacKenzie, F., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Bochkarev, A., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description