9NAQ | pdb_00009naq

Cryo-EM structure of 110_C4 Fab in complex with CIDRa1.7 PfEMP1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Identification of broadly inhibitory anti-PfEMP1 antibodies by mass spectrometry sequencing of plasma IgG from a malaria-exposed child.

Turner, L.Nunez de Villavicencio Diaz, T.Raghavan, S.S.R.Kana, I.H.Lyimo, E.Reitzel, C.Wang, C.W.Berube, E.Jensen, R.W.Loeffler, J.R.Fernandez-Quintero, M.L.Theander, T.G.Lusingu, J.P.A.Le Bihan, T.Han, X.Minja, D.T.R.Ward, A.B.Ma, B.Lavstsen, T.

(2025) Proc Natl Acad Sci U S A 122: e2508744122-e2508744122

  • DOI: https://doi.org/10.1073/pnas.2508744122
  • Primary Citation of Related Structures:  
    9NAQ

  • PubMed Abstract: 

    Plasmodium falciparum pathology is driven by the accumulation of parasite-infected erythrocytes in blood capillaries. This sequestration process is mediated by the parasite's P. falciparum erythrocyte membrane protein 1 (PfEMP1) adhesins, which bind select endothelial cell receptors. A subset of PfEMP1 binding human endothelial protein C receptor (EPCR) through their cysteine-rich interdomain region alpha 1 (CIDRα1) domains drives the pathogenesis to severe malaria. Despite high sequence diversity among CIDRα1 domains, individuals living in malaria-endemic regions become immune to severe disease in part through acquisition of antibodies inhibiting the PfEMP1-EPCR interaction. Here, we demonstrate an approach to identify pathogen-specific human monoclonal antibodies from plasma, combining mass spectrometry analysis of antigen-purified polyclonal plasma IgG and Ig transcript sequencing. We identified a clonal family of broadly reactive and EPCR binding-inhibitory human monoclonal antibodies against CIDRα1. The antibodies, isolated from a 9-y-old child, exhibited potent inhibition of EPCR binding broadly across CIDRα1 domains as well as binding of infected erythrocytes to EPCR. Structural analysis of one antibody variant complexed with CIDRα1 revealed a shared epitope of the clonal antibody family overlapping the EPCR binding site and the epitopes of two previously identified monoclonal antibodies, C7 and C74, with similar functional patterns. However, although C7, C74, and 110-3 antibodies all depend on the same few residues conserved in CIDRα1 to retain EPCR binding, the 110-3 antibodies contact additional variable residues, reducing their breadth of reactivity across the CIDRα1 family. These data bolster the hypothesis that broadly inhibitory antibodies against severe malaria-associated PfEMP1 target similar epitopes and are commonly developed in malaria-exposed individuals.


  • Organizational Affiliation
    • Centre for Translational Medicine and Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen 2200, Denmark.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
110_C4 Fab heavy chainA [auth H]122Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
110_C4 Fab light chainB [auth L]111Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Erythrocyte membrane protein 1C [auth A]1,195Plasmodium falciparumMutation(s): 0 
Gene Names: IT4_var22
UniProt
Find proteins for A3R6S4 (Plasmodium falciparum)
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Go to UniProtKB:  A3R6S4
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UniProt GroupA3R6S4
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited States--
Novo Nordisk FoundationDenmark--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release