4EOY

Plasmodium falciparum Atg8 in complex with Plasmodium falciparum Atg3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report



Literature

Structural characterization and inhibition of the Plasmodium Atg8-Atg3 interaction.

Hain, A.U.Weltzer, R.R.Hammond, H.Jayabalasingham, B.Dinglasan, R.R.Graham, D.R.Colquhoun, D.R.Coppens, I.Bosch, J.

(2012) J Struct Biol 180: 551-562

  • DOI: 10.1016/j.jsb.2012.09.001
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The autophagy-related proteins are thought to serve multiple functions in Plasmodium and are considered essential to parasite survival and development. We have studied two key interacting proteins, Atg8 and Atg3, of the autophagy pathway in Plasmodiu ...

    The autophagy-related proteins are thought to serve multiple functions in Plasmodium and are considered essential to parasite survival and development. We have studied two key interacting proteins, Atg8 and Atg3, of the autophagy pathway in Plasmodium falciparum. These proteins are vital for the formation and elongation of the autophagosome and essential to the process of macroautophagy. Autophagy may be required for conversion of the sporozoite into erythrocytic-infective merozoites and may be crucial for other functions during asexual blood stages. Here we describe the identification of an Atg8 family interacting motif (AIM) in Plasmodium Atg3, which binds Plasmodium Atg8. We determined the co-crystal structure of PfAtg8 with a short Atg3¹⁰³⁻¹¹⁰ peptide, corresponding to this motif, to 2.2 Å resolution. Our in vitro interaction studies are in agreement with our X-ray crystal structure. Furthermore they suggest an important role for a unique Apicomplexan loop absent from human Atg8 homologues. Prevention of the protein-protein interaction of full length PfAtg8 with PfAtg3 was achieved at low micromolar concentrations with a small molecule, 1,2,3-trihydroxybenzene. Together our structural and interaction studies represent a starting point for future antimalarial drug discovery and design for this novel protein-protein interaction.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Microtubule-associated protein 1 light chain 3A, B, C128Plasmodium falciparum 3D7Mutation(s): 3 
Gene Names: PF10_0193PF3D7_1019900
Find proteins for Q8IJK2 (Plasmodium falciparum (isolate 3D7))
Explore Q8IJK2 
Go to UniProtKB:  Q8IJK2
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Autophagy-related protein 3D, E, F8Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0905700.2
Find proteins for C0H519 (Plasmodium falciparum (isolate 3D7))
Explore C0H519 
Go to UniProtKB:  C0H519
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, C, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.3α = 90
b = 111.08β = 92.58
c = 57.09γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-20
    Type: Initial release