9CR9 | pdb_00009cr9

Crystal structure of MA6 Fab in complex with PfCSP repeat region peptide NPNA3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.215 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Repertoire, function, and structure of serological antibodies induced by the R21/Matrix-M malaria vaccine.

McDaniel, J.R.Voss, W.N.Bowyer, G.Rush, S.A.Spencer, A.J.Bellamy, D.Ulaszewska, M.Goike, J.Gregory, S.King, C.R.McLellan, J.S.Hill, A.V.S.Georgiou, G.Ewer, K.J.Ippolito, G.C.

(2025) J Exp Medicine 222

  • DOI: https://doi.org/10.1084/jem.20241908
  • Primary Citation Related Structures: 
    9CR9

  • PubMed Abstract: 

    The World Health Organization (WHO) recently recommended the programmatic use of the R21/Matrix-M vaccine for Plasmodium falciparum malaria prevention in children living in malaria-endemic areas. To determine its effects on humoral immunity, we conducted a proteomic analysis of polyclonal IgG antibodies directed against the NANP tetrapeptide of the circumsporozoite protein (CSP), which comprises the vaccine's core immunogen. In 10 malaria-naïve adult volunteers, R21/Matrix-M induced polarized IgG anti-NANP repertoires, heavily skewed for IGHV3-30/3-33 genes bearing minimal somatic mutation, which remained static in composition following a controlled human malaria infection challenge. Notably, these vaccine-generated antibodies cross-reacted with another protective CSP epitope, the N-terminal junction region, despite its absence from the R21 construct. NANP-specific IGHV3-30/3-33 mAbs mined from polyclonal IgG repertoires blocked sporozoite invasion in vitro and prevented parasitemia in vivo. Overall, R21/Matrix-M elicits polarized, minimally mutated, polyclonal IgG responses that can target multiple protective CSP epitopes, offering molecular insight into the serological basis for its demonstrated efficacy against P. falciparum malaria.


  • Organizational Affiliation
    • The University of Texas at Austin , Austin, TX, USA.

Macromolecule Content 

  • Total Structure Weight: 99.47 kDa 
  • Atom Count: 7,814 
  • Modeled Residue Count: 872 
  • Deposited Residue Count: 920 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MA6 Fab heavy chainA,
D [auth H]
235Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
MA6 Fab light chainB,
E [auth L]
213Homo sapiensMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Circumsporozoite protein (NPNA)3 repeat region peptideC,
F [auth P]
12Plasmodium falciparumMutation(s): 0 
UniProt
Find proteins for P05691 (Plasmodium falciparum (isolate le5))
Explore P05691 
Go to UniProtKB:  P05691
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05691
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.6α = 90
b = 61.05β = 90
c = 152.999γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references