7PHW | pdb_00007phw

PfCyRPA bound to monoclonal antibody Cy.004 Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 
    0.277 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7PHW

This is version 1.3 of the entry. See complete history

Literature

Heterotypic interactions drive antibody synergy against a malaria vaccine candidate.

Ragotte, R.J.Pulido, D.Lias, A.M.Quinkert, D.Alanine, D.G.W.Jamwal, A.Davies, H.Nacer, A.Lowe, E.D.Grime, G.W.Illingworth, J.J.Donat, R.F.Garman, E.F.Bowyer, P.W.Higgins, M.K.Draper, S.J.

(2022) Nat Commun 13: 933-933

  • DOI: https://doi.org/10.1038/s41467-022-28601-4
  • Primary Citation Related Structures: 
    7PHU, 7PHV, 7PHW, 7PI2, 7PI3, 7PI7

  • PubMed Abstract: 

    Understanding mechanisms of antibody synergy is important for vaccine design and antibody cocktail development. Examples of synergy between antibodies are well-documented, but the mechanisms underlying these relationships often remain poorly understood. The leading blood-stage malaria vaccine candidate, CyRPA, is essential for invasion of Plasmodium falciparum into human erythrocytes. Here we present a panel of anti-CyRPA monoclonal antibodies that strongly inhibit parasite growth in in vitro assays. Structural studies show that growth-inhibitory antibodies bind epitopes on a single face of CyRPA. We also show that pairs of non-competing inhibitory antibodies have strongly synergistic growth-inhibitory activity. These antibodies bind to neighbouring epitopes on CyRPA and form lateral, heterotypic interactions which slow antibody dissociation. We predict that such heterotypic interactions will be a feature of many immune responses. Immunogens which elicit such synergistic antibody mixtures could increase the potency of vaccine-elicited responses to provide robust and long-lived immunity against challenging disease targets.


  • Organizational Affiliation
    • Department of Biochemistry, University of Oxford, Oxford, UK.

Macromolecule Content 

  • Total Structure Weight: 193.77 kDa 
  • Atom Count: 11,683 
  • Modeled Residue Count: 1,494 
  • Deposited Residue Count: 1,746 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cysteine-rich protective antigen
A, D
343Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: CyRPApfd1130wPF3D7_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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Monoclonal antibody Cy.004 heavy chain
B, E
321Gallus gallusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Monoclonal antibody Cy.004 light chain
C, F
209Gallus gallusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free:  0.277 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.057α = 90
b = 80.316β = 115.23
c = 114.91γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary