5EZI | pdb_00005ezi

Crystal Structure of Fab of parasite invasion inhibitory antibody c1 - hexagonal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 
    0.221 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.195 (Depositor) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 5EZI

This is version 2.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 49.02 kDa 
  • Atom Count: 3,923 
  • Modeled Residue Count: 436 
  • Deposited Residue Count: 436 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab c12 heavy chainA [auth H]222Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab c12 Light chainB [auth L]214Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth A]9N-Glycosylation
Glycosylation Resources
GlyTouCan: G58667NI
GlyCosmos: G58667NI
GlyGen: G58667NI

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth H]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free:  0.221 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.195 (Depositor) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.7α = 90
b = 82.7β = 90
c = 361.88γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Structure summary
  • Version 1.2: 2017-03-01
    Changes: Structure summary
  • Version 1.3: 2017-04-26
    Changes: Other, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary