4CBW

Crystal structure of Plasmodium berghei actin I with D-loop from muscle actin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1371/journal.ppat.1004091
  • Primary Citation of 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.


  • Organizational Affiliation

    Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACTIN, ALPHA SKELETAL MUSCLE, ACTIN377Plasmodium bergheisynthetic constructMutation(s): 0 
UniProt
Find proteins for P68137 (Sus scrofa)
Explore P68137 
Go to UniProtKB:  P68137
Find proteins for Q4Z1L3 (Plasmodium berghei (strain Anka))
Explore Q4Z1L3 
Go to UniProtKB:  Q4Z1L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ4Z1L3P68137
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GELSOLINB [auth G]127Mus musculusMutation(s): 0 
UniProt
Find proteins for P13020 (Mus musculus)
Explore P13020 
Go to UniProtKB:  P13020
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13020
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.24α = 90
b = 69.53β = 90
c = 178.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2014-05-14
    Changes: Data collection
  • Version 1.2: 2017-03-15
    Changes: Source and taxonomy
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Other
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description