4CBX | pdb_00004cbx

Crystal structure of Plasmodium berghei actin II

• PDB DOI: https://doi.org/10.2210/pdb4CBX/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Plasmodium berghei, Mus musculus
• Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-10-17 Released: 2014-04-30 
• Deposition Author(s): Vahokoski, J., Bhargav, S.P., Desfosses, A., Andreadaki, M., Kumpula, E.P., Ignatev, A., Munico Martinez, S., Lepper, S., Frischknecht, F., Siden-Kiamos, I., Sachse, C., Kursula, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structural Differences Explain Diverse Functions of Plasmodium Actins.

Vahokoski, J., Bhargav, S.P., Desfosses, A., Andreadaki, M., Kumpula, E., Martinez, S.M., Ignatev, A., Lepper, S., Frischknecht, F., Siden-Kiamos, I., Sachse, C., Kursula, I.

(2014) PLoS Pathog 10: 4091

• PubMed: 24743229 
• DOI: https://doi.org/10.1371/journal.ppat.1004091
• Primary Citation Related Structures: 
  4CBU, 4CBW, 4CBX


• PubMed Abstract: 
  

  Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also differ from each other more than isoforms in any other species. Microfilaments have not been directly observed in Plasmodium and are presumed to be short and highly dynamic. We show that actin I cannot complement actin II in male gametogenesis, suggesting critical structural differences. Cryo-EM reveals that Plasmodium actin I has a unique filament structure, whereas actin II filaments resemble canonical F-actin. Both Plasmodium actins hydrolyze ATP more efficiently than α-actin, and unlike any other actin, both parasite actins rapidly form short oligomers induced by ADP. Crystal structures of both isoforms pinpoint several structural changes in the monomers causing the unique polymerization properties. Inserting the canonical D-loop to Plasmodium actin I leads to the formation of long filaments in vitro. In vivo, this chimera restores gametogenesis in parasites lacking actin II, suggesting that stable filaments are required for exflagellation. Together, these data underline the divergence of eukaryotic actins and demonstrate how structural differences in the monomers translate into filaments with different properties, implying that even eukaryotic actins have faced different evolutionary pressures and followed different paths for developing their polymerization properties.

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Organizational Affiliation: 
• Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Crete, Greece.
Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Centre for Structural Systems Biology; Helmholtz Centre for Infection Research and German Electron Synchrotron, Hamburg, Germany.
Parasitology - Department of Infectious Diseases, University of Heidelberg Medical School, Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 58.01 kDa 
• Atom Count: 4,338 
• Modeled Residue Count: 480 
• Deposited Residue Count: 505 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIN-2	A	378	Plasmodium berghei	Mutation(s): 0  EC: 3.6.4
UniProt
Find proteins for Q4YU79 (Plasmodium berghei (strain Anka)) Explore Q4YU79  Go to UniProtKB:  Q4YU79

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GELSOLIN	B [auth G]	127	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P13020 (Mus musculus) Explore P13020  Go to UniProtKB:  P13020

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	H [auth G]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	G [auth A], I [auth G], J [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.248	α = 90
b = 60.908	β = 97.24
c = 75.518	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PROTEUM2	data reduction
PROTEUM2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Vahokoski, J., Bhargav, S.P., Desfosses, A., Andreadaki, M., Kumpula, E.P., Ignatev, A., Munico Martinez, S., Lepper, S., Frischknecht, F., Siden-Kiamos, I., Sachse, C., Kursula, I.

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Data collection
• Version 1.2: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description