5EZN

Crystal Structure of PfCyRPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the malaria vaccine candidate antigen CyRPA and its complex with a parasite invasion inhibitory antibody.

Favuzza, P.Guffart, E.Tamborrini, M.Scherer, B.Dreyer, A.M.Rufer, A.C.Erny, J.Hoernschemeyer, J.Thoma, R.Schmid, G.Gsell, B.Lamelas, A.Benz, J.Joseph, C.Matile, H.Pluschke, G.Rudolph, M.G.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.20383
  • Primary Citation of Related Structures:  
    5EZI, 5EZJ, 5EZL, 5EZN, 5EZO

  • PubMed Abstract: 

    Invasion of erythrocytes by Plasmodial merozoites is a composite process involving the interplay of several proteins. Among them, the Plasmodium falciparum Cysteine-Rich Protective Antigen (PfCyRPA) is a crucial component of a ternary complex, including Reticulocyte binding-like Homologous protein 5 (PfRH5) and the RH5-interacting protein (PfRipr), essential for erythrocyte invasion. Here, we present the crystal structures of PfCyRPA and its complex with the antigen-binding fragment of a parasite growth inhibitory antibody. PfCyRPA adopts a 6-bladed β-propeller structure with similarity to the classic sialidase fold, but it has no sialidase activity and fulfills a purely non-enzymatic function. Characterization of the epitope recognized by protective antibodies may facilitate design of peptidomimetics to focus vaccine responses on protective epitopes. Both in vitro and in vivo anti-PfCyRPA and anti-PfRH5 antibodies showed more potent parasite growth inhibitory activity in combination than on their own, supporting a combined delivery of PfCyRPA and PfRH5 in vaccines.


  • Organizational Affiliation

    Medical Parasitology and Infection Biology Department, Swiss Tropical and Public Health Institute, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine-rich protective antigen157Plasmodium falciparum 3D7Mutation(s): 1 
Gene Names: PF3D7_0423800
UniProt
Find proteins for Q8IFM8 (Plasmodium falciparum (isolate 3D7))
Explore Q8IFM8 
Go to UniProtKB:  Q8IFM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IFM8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine-rich protective antigenB [auth E]176Plasmodium falciparum 3D7Mutation(s): 2 
Gene Names: PF3D7_0423800
UniProt
Find proteins for Q8IFM8 (Plasmodium falciparum (isolate 3D7))
Explore Q8IFM8 
Go to UniProtKB:  Q8IFM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IFM8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine-rich protective antigenC [auth B]161Plasmodium falciparum 3D7Mutation(s): 1 
Gene Names: PF3D7_0423800
UniProt
Find proteins for Q8IFM8 (Plasmodium falciparum (isolate 3D7))
Explore Q8IFM8 
Go to UniProtKB:  Q8IFM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IFM8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine-rich protective antigenD [auth G]170Plasmodium falciparum 3D7Mutation(s): 1 
Gene Names: PF3D7_0423800
UniProt
Find proteins for Q8IFM8 (Plasmodium falciparum (isolate 3D7))
Explore Q8IFM8 
Go to UniProtKB:  Q8IFM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IFM8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.24α = 90
b = 78.5β = 94.85
c = 97.04γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Structure summary
  • Version 1.2: 2017-04-26
    Changes: Other, Structure summary
  • Version 1.3: 2017-10-11
    Changes: Data collection
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description