8EKF

X-ray crystal structure of 311R Fab in complex with the PfCSP peptide NPNA-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Affinity-matured homotypic interactions induce spectrum of PfCSP structures that influence protection from malaria infection.

Martin, G.M.Torres, J.L.Pholcharee, T.Oyen, D.Flores-Garcia, Y.Gibson, G.Moskovitz, R.Beutler, N.Jung, D.D.Copps, J.Lee, W.H.Gonzalez-Paez, G.Emerling, D.MacGill, R.S.Locke, E.King, C.R.Zavala, F.Wilson, I.A.Ward, A.B.

(2023) Nat Commun 14: 4546-4546

  • DOI: https://doi.org/10.1038/s41467-023-40151-x
  • Primary Citation of Related Structures:  
    8DYT, 8DYW, 8DYX, 8DYY, 8DZ3, 8DZ4, 8DZ5, 8EKF

  • PubMed Abstract: 

    The generation of high-quality antibody responses to Plasmodium falciparum (Pf) circumsporozoite protein (PfCSP), the primary surface antigen of Pf sporozoites, is paramount to the development of an effective malaria vaccine. Here we present an in-depth structural and functional analysis of a panel of potent antibodies encoded by the immunoglobulin heavy chain variable (IGHV) gene IGHV3-33, which is among the most prevalent and potent antibody families induced in the anti-PfCSP immune response and targets the Asn-Ala-Asn-Pro (NANP) repeat region. Cryo-electron microscopy (cryo-EM) reveals a remarkable spectrum of helical antibody-PfCSP structures stabilized by homotypic interactions between tightly packed fragments antigen binding (Fabs), many of which correlate with somatic hypermutation. We demonstrate a key role of these mutated homotypic contacts for high avidity binding to PfCSP and in protection from Pf malaria infection. Together, these data emphasize the importance of anti-homotypic affinity maturation in the frequent selection of IGHV3-33 antibodies and highlight key features underlying the potent protection of this antibody family.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
311R Heavy ChainA [auth HHH]224Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
311R Light ChainB [auth LLL]218Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PfCSP peptide NPNA-3C [auth CCC]12Plasmodium falciparum 3D7Mutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.412α = 90
b = 70.765β = 90
c = 170.246γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PHASERphasing
Aimlessdata reduction
pointlessdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-01
    Changes: Database references