7UYL | pdb_00007uyl

850 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.212 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7UYL

This is version 2.2 of the entry. See complete history

Literature

High-density binding to Plasmodium falciparum circumsporozoite protein repeats by inhibitory antibody elicited in mouse with human immunoglobulin repertoire.

Kucharska, I.Binter, S.Murugan, R.Scally, S.W.Ludwig, J.Prieto, K.Thai, E.Costa, G.Li, K.Horn, G.Q.Flores-Garcia, Y.Bosch, A.Sicard, T.Rubinstein, J.L.Zavala, F.Dennison, S.M.Tomaras, G.D.Levashina, E.A.Kellam, P.Wardemann, H.Julien, J.P.

(2022) PLoS Pathog 18: e1010999-e1010999

  • DOI: https://doi.org/10.1371/journal.ppat.1010999
  • Primary Citation Related Structures: 
    7UYL, 7UYM, 7V05

  • PubMed Abstract: 

    Antibodies targeting the human malaria parasite Plasmodium falciparum circumsporozoite protein (PfCSP) can prevent infection and disease. PfCSP contains multiple central repeating NANP motifs; some of the most potent anti-infective antibodies against malaria bind to these repeats. Multiple antibodies can bind the repeating epitopes concurrently by engaging into homotypic Fab-Fab interactions, which results in the ordering of the otherwise largely disordered central repeat into a spiral. Here, we characterize IGHV3-33/IGKV1-5-encoded monoclonal antibody (mAb) 850 elicited by immunization of transgenic mice with human immunoglobulin loci. mAb 850 binds repeating NANP motifs with picomolar affinity, potently inhibits Plasmodium falciparum (Pf) in vitro and, when passively administered in a mouse challenge model, reduces liver burden to a similar extent as some of the most potent anti-PfCSP mAbs yet described. Like other IGHV3-33/IGKV1-5-encoded anti-NANP antibodies, mAb 850 primarily utilizes its HCDR3 and germline-encoded aromatic residues to recognize its core NANP motif. Biophysical and cryo-electron microscopy analyses reveal that up to 19 copies of Fab 850 can bind the PfCSP repeat simultaneously, and extensive homotypic interactions are observed between densely-packed PfCSP-bound Fabs to indirectly improve affinity to the antigen. Together, our study expands on the molecular understanding of repeat-induced homotypic interactions in the B cell response against PfCSP for potently protective mAbs against Pf infection.


  • Organizational Affiliation
    • Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Canada.

Macromolecule Content 

  • Total Structure Weight: 59.4 kDa 
  • Atom Count: 4,492 
  • Modeled Residue Count: 559 
  • Deposited Residue Count: 560 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
850 Fab Heavy ChainA [auth H]226Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
850 Fab Light ChainB [auth L]213Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
VHH nanobodyC [auth K]121Lama glamaMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.212 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.18α = 90
b = 137.18β = 90
c = 63.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XPREPdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ontario Early Researcher AwardsCanada--
Canada Foundation for InnovationCanada--
Ontario Research FundCanada--
Canada Research ChairsCanada--
Bill & Melinda Gates FoundationUnited StatesINV-008866
CIFAR Azrieli Global ScholarsCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 2.0: 2022-12-21
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 2.2: 2024-11-20
    Changes: Structure summary