8C67 | pdb_00008c67

Crystal structure of Ab25 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.255 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The hinge-engineered IgG1-IgG3 hybrid subclass IgGh 47 potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 antibodies.

Izadi, A.Karami, Y.Bratanis, E.Wrighton, S.Khakzad, H.Nyblom, M.Olofsson, B.Happonen, L.Tang, D.Sundwall, M.Godzwon, M.Chao, Y.Toledo, A.G.Schmidt, T.Ohlin, M.Nilges, M.Malmstrom, J.Bahnan, W.Shannon, O.Malmstrom, L.Nordenfelt, P.

(2024) Nat Commun 15: 3600-3600

  • DOI: https://doi.org/10.1038/s41467-024-47928-8
  • Primary Citation of Related Structures:  
    8C67

  • PubMed Abstract: 

    Streptococcus pyogenes can cause invasive disease with high mortality despite adequate antibiotic treatments. To address this unmet need, we have previously generated an opsonic IgG1 monoclonal antibody, Ab25, targeting the bacterial M protein. Here, we engineer the IgG2-4 subclasses of Ab25. Despite having reduced binding, the IgG3 version promotes stronger phagocytosis of bacteria. Using atomic simulations, we show that IgG3's Fc tail has extensive movement in 3D space due to its extended hinge region, possibly facilitating interactions with immune cells. We replaced the hinge of IgG1 with four different IgG3-hinge segment subclasses, IgGh xx . Hinge-engineering does not diminish binding as with IgG3 but enhances opsonic function, where a 47 amino acid hinge is comparable to IgG3 in function. IgGh 47 shows improved protection against S. pyogenes in a systemic infection mouse model, suggesting that IgGh 47 has promise as a preclinical therapeutic candidate. Importantly, the enhanced opsonic function of IgGh 47 is generalizable to diverse S. pyogenes strains from clinical isolates. We generated IgGh 47 versions of anti-SARS-CoV-2 mAbs to broaden the biological applicability, and these also exhibit strongly enhanced opsonic function compared to the IgG1 subclass. The improved function of the IgGh 47 subclass in two distant biological systems provides new insights into antibody function.


  • Organizational Affiliation
    • Department of Clinical Sciences Lund, Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
antibody 25 heavy chainA [auth H],
C [auth A],
E [auth C],
G [auth E]
229Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
antibody 25 light chainB [auth L],
D [auth B],
F [auth D],
H [auth F]
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.897α = 90
b = 71.89β = 90.102
c = 146.014γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Database references, Structure summary