8A64 | pdb_00008a64

cryoEM structure of the catalytically inactive EndoS from S. pyogenes in complex with the Fc region of immunoglobulin G1.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8A64

This is version 1.3 of the entry. See complete history

Literature

Mechanism of antibody-specific deglycosylation and immune evasion by Streptococcal IgG-specific endoglycosidases.

Trastoy, B.Du, J.J.Cifuente, J.O.Rudolph, L.Garcia-Alija, M.Klontz, E.H.Deredge, D.Sultana, N.Huynh, C.G.Flowers, M.W.Li, C.Sastre, D.E.Wang, L.X.Corzana, F.Mallagaray, A.Sundberg, E.J.Guerin, M.E.

(2023) Nat Commun 14: 1705-1705

  • DOI: https://doi.org/10.1038/s41467-023-37215-3
  • Primary Citation Related Structures: 
    8A64

  • PubMed Abstract: 

    Bacterial pathogens have evolved intricate mechanisms to evade the human immune system, including the production of immunomodulatory enzymes. Streptococcus pyogenes serotypes secrete two multi-modular endo-β-N-acetylglucosaminidases, EndoS and EndoS2, that specifically deglycosylate the conserved N-glycan at Asn297 on IgG Fc, disabling antibody-mediated effector functions. Amongst thousands of known carbohydrate-active enzymes, EndoS and EndoS2 represent just a handful of enzymes that are specific to the protein portion of the glycoprotein substrate, not just the glycan component. Here, we present the cryoEM structure of EndoS in complex with the IgG1 Fc fragment. In combination with small-angle X-ray scattering, alanine scanning mutagenesis, hydrolytic activity measurements, enzyme kinetics, nuclear magnetic resonance and molecular dynamics analyses, we establish the mechanisms of recognition and specific deglycosylation of IgG antibodies by EndoS and EndoS2. Our results provide a rational basis from which to engineer novel enzymes with antibody and glycan selectivity for clinical and biotechnological applications.


  • Organizational Affiliation
    • Structural Glycobiology Laboratory, Biocruces Health Research Institute, Barakaldo, Bizkaia, 48903, Spain. beatriz.trastoy@gmail.com.

Macromolecule Content 

  • Total Structure Weight: 207.66 kDa 
  • Atom Count: 6,737 
  • Modeled Residue Count: 1,354 
  • Deposited Residue Count: 1,858 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endo-beta-N-acetylglucosaminidase F2960Streptococcus pyogenesMutation(s): 1 
Gene Names: endoSM1GAS476_1618
EC: 3.2.1.96
UniProt
Find proteins for Q99Y92 (Streptococcus pyogenes serotype M1)
Explore Q99Y92 
Go to UniProtKB:  Q99Y92
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99Y92
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin gamma-1 heavy chain
B, C
449Homo sapiensMutation(s): 0 
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
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

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 States1R01AI149297-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Structure summary
  • Version 1.2: 2023-07-26
    Changes: Other
  • Version 1.3: 2024-11-20
    Changes: Data collection, Refinement description, Structure summary