8URO | pdb_00008uro

Crystal structure of IgG1-Fc fragment (E382S) in complex with Corynebacterial ENGase CU43 (D187A-E189A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.62 Å
  • R-Value Free: 
    0.369 (Depositor), 0.369 (DCC) 
  • R-Value Work: 
    0.334 (Depositor), 0.334 (DCC) 
  • R-Value Observed: 
    0.336 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

The mechanistic basis for interprotomer deglycosylation of antibodies by corynebacterial IgG-specific endoglycosidases.

Sastre, D.E.Bournazos, S.Huliciak, M.Grace, B.A.C.Boder, E.J.Du, J.Sultana, N.Azzam, T.Brown, T.J.Flowers, M.W.Lollar, P.Xu, T.Chernova, T.A.Keith, A.D.Keen, M.Saltzman, A.Martinez Gascuena, A.Trastoy, B.Guerin, M.E.Frank, F.Ortlund, E.A.Ravetch, J.V.Sundberg, E.J.

(2025) Nat Commun 16: 6147-6147

  • DOI: https://doi.org/10.1038/s41467-025-60986-w
  • Primary Citation Related Structures: 
    8URO

  • PubMed Abstract: 

    Corynebacterium diphtheriae clade species secrete single-domain endo-β-N-acetylglucosaminidases (ENGases) that specifically bind to human IgG antibodies and hydrolyze their N297-linked glycans. Here, we define the molecular mechanisms of IgG-specific deglycosylation for the entire family of corynebacterial IgG-specific ENGases, including but not limited to CU43 and CM49. By solving the crystal structure of CU43 in a 1:1 complex with the IgG1 Fc region, combined with targeted and saturation mutagenesis analysis and activity measurements using engineered antibodies, we establish an inter-protomeric mechanism of recognition and deglycosylation of IgG antibodies. Using in silico modeling, small-angle X-ray scattering and saturation mutagenesis we determine that CM49 uses a unique binding site on the Fc region, to process N297-linked glycans. Moreover, we demonstrate that CU43 treatment is highly effective in abrogating Fc effector functions in humanized mouse models, while preserving the neutralizing capacity of anti-influenza IgG antibodies, thereby conferring protection against lethal influenza challenge.


  • Organizational Affiliation
    • Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA. dsastre@emory.edu.

Macromolecule Content 

  • Total Structure Weight: 196.55 kDa 
  • Atom Count: 9,190 
  • Modeled Residue Count: 1,383 
  • Deposited Residue Count: 1,758 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Corynebacterial protease CP40
A, D
415Corynebacterium ulceransMutation(s): 2 
Gene Names: cppCULC0211_20780
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin gamma-1 heavy chain
B, C, E, F
232Homo sapiensMutation(s): 1 
UniProt
Find proteins for P0DOX5 (Homo sapiens)
Explore P0DOX5 
Go to UniProtKB:  P0DOX5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOX5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.62 Å
  • R-Value Free:  0.369 (Depositor), 0.369 (DCC) 
  • R-Value Work:  0.334 (Depositor), 0.334 (DCC) 
  • R-Value Observed: 0.336 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.439α = 90
b = 81.991β = 113.2
c = 148.099γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI149297

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Database references
  • Version 1.2: 2026-02-11
    Changes: Database references