8F9S

Crystal structure of Ky15.2 Fab in complex with circumsporozoite protein NDN peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein.

Thai, E.Murugan, R.Binter, S.Burn Aschner, C.Prieto, K.Kassardjian, A.Obraztsova, A.S.Kang, R.W.Flores-Garcia, Y.Mathis-Torres, S.Li, K.Horn, G.Q.Huntwork, R.H.C.Bolscher, J.M.de Bruijni, M.H.C.Sauerwein, R.Dennison, S.M.Tomaras, G.D.Zavala, F.Kellam, P.Wardemann, H.Julien, J.P.

(2023) Cell Rep 42: 113330-113330

  • DOI: https://doi.org/10.1016/j.celrep.2023.113330
  • Primary Citation of Related Structures:  
    8F95, 8F9E, 8F9F, 8F9S, 8F9T, 8F9U, 8F9V, 8F9W, 8FA6, 8FA7, 8FA8, 8FA9, 8FAN, 8FAS, 8FAT, 8FB5, 8FB6, 8FB7, 8FB8, 8FBA, 8FDC, 8FDD

  • PubMed Abstract: 

    IGHV3-33-encoded antibodies are prevalent in the human humoral response against the Plasmodium falciparum circumsporozoite protein (PfCSP). Among VH3-33 antibodies, cross-reactivity between PfCSP major repeat (NANP), minor (NVDP), and junctional (NPDP) motifs is associated with high affinity and potent parasite inhibition. However, the molecular basis of antibody cross-reactivity and the relationship with efficacy remain unresolved. Here, we perform an extensive structure-function characterization of 12 VH3-33 anti-PfCSP monoclonal antibodies (mAbs) with varying degrees of cross-reactivity induced by immunization of mice expressing a human immunoglobulin gene repertoire. We identify residues in the antibody paratope that mediate cross-reactive binding and delineate four distinct epitope conformations induced by antibody binding, with one consistently associated with high protective efficacy and another that confers comparably potent inhibition of parasite liver invasion. Our data show a link between molecular features of cross-reactive VH3-33 mAb binding to PfCSP and mAb potency, relevant for the development of antibody-based interventions against malaria.


  • Organizational Affiliation

    Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ky15.2 Antibody, heavy chainA [auth H],
C [auth A]
226Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ky15.2 Antibody, light chainB [auth L],
D [auth B]
213Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Circumsporozoite protein NDN peptideE [auth C],
F [auth P]
12Plasmodium falciparum NF54Mutation(s): 0 
UniProt
Find proteins for P19597 (Plasmodium falciparum (isolate NF54))
Explore P19597 
Go to UniProtKB:  P19597
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19597
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth H]
H
I [auth L]
J [auth L]
K [auth L]
G [auth H],
H,
I [auth L],
J [auth L],
K [auth L],
L,
M [auth A],
N [auth A],
O [auth A],
P [auth B],
Q [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.479α = 90
b = 77.853β = 91.68
c = 123.649γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1179906

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Source and taxonomy