2XFA | pdb_00002xfa

Crystal structure of Plasmodium berghei actin depolymerization factor 2

• PDB DOI: https://doi.org/10.2210/pdb2XFA/pdb

• Classification: PROTEIN BINDING
• Organism(s): Plasmodium berghei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-21 Released: 2011-06-15 
• Deposition Author(s): Singh, B.K., Sattler, J.M., Huttu, J., Chatterjee, M., Schueler, H., Kursula, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.245 (Depositor) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Models: experimental

Literature

Crystal Structures Explain Functional Differences in the Two Actin Depolymerization Factors of the Malaria Parasite.

Singh, B.K., Sattler, J.M., Chatterjee, M., Huttu, J., Schuler, H., Kursula, I.

(2011) J Biological Chem 286: 28256

• PubMed: 21832095 
• DOI: https://doi.org/10.1074/jbc.M111.211730
• Primary Citation Related Structures: 
  2XF1, 2XFA


• PubMed Abstract: 
  

  Apicomplexan parasites, such as the malaria-causing Plasmodium, utilize an actin-based motor for motility and host cell invasion. The actin filaments of these parasites are unusually short, and actin polymerization is under strict control of a small set of regulatory proteins, which are poorly conserved with their mammalian orthologs. Actin depolymerization factors (ADFs) are among the most important actin regulators, affecting the rates of filament turnover in a multifaceted manner. Plasmodium has two ADFs that display low sequence homology with each other and with the higher eukaryotic family members. Here, we show that ADF2, like canonical ADF proteins but unlike ADF1, binds to both globular and filamentous actin, severing filaments and inducing nucleotide exchange on the actin monomer. The crystal structure of Plasmodium ADF1 shows major differences from the ADF consensus, explaining the lack of F-actin binding. Plasmodium ADF2 structurally resembles the canonical members of the ADF/cofilin family.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oulu, PO Box 3000, 90014 Oulu, Finland.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.3 kDa 
• Atom Count: 2,369 
• Modeled Residue Count: 286 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIN DEPOLYMERIZATION FACTOR 2	A, B	148	Plasmodium berghei	Mutation(s): 0
UniProt
Find proteins for Q3YPH0 (Plasmodium berghei) Explore Q3YPH0  Go to UniProtKB:  Q3YPH0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.245 (Depositor) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.58	α = 90
b = 57.9	β = 90
c = 40.49	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-15 
Deposition Author(s): Singh, B.K., Sattler, J.M., Huttu, J., Chatterjee, M., Schueler, H., Kursula, I.

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-08-31
  Changes: Database references, Refinement description, Version format compliance
• Version 1.2: 2018-01-17
  Changes: Data collection
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description