7K7I

Density-fitted Model Structure of Antibody Variable Domains of TyTx4 in Complex with PltB pentamer of Typhoid Toxin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structural basis of Salmonella A 2 B 5 toxin neutralization by antibodies targeting the glycan-receptor binding subunits.

Nguyen, T.Richards, A.F.Neupane, D.P.Feathers, J.R.Yang, Y.A.Sim, J.H.Byun, H.Lee, S.Ahn, C.Van Slyke, G.Fromme, J.C.Mantis, N.J.Song, J.

(2021) Cell Rep 36: 109654-109654

  • DOI: https://doi.org/10.1016/j.celrep.2021.109654
  • Primary Citation of Related Structures:  
    7K7H, 7K7I

  • PubMed Abstract: 

    Many bacterial pathogens secrete A (2) B 5 toxins comprising two functionally distinct yet complementary "A" and "B" subunits to benefit the pathogens during infection. The lectin-like pentameric B subunits recognize specific sets of host glycans to deliver the toxin into target host cells. Here, we offer the molecular mechanism by which neutralizing antibodies, which have the potential to bind to all glycan-receptor binding sites and thus completely inhibit toxin binding to host cells, are inhibited from exerting this action. Cryogenic electron microscopy (cryo-EM)-based analyses indicate that the skewed positioning of the toxin A subunit(s) toward one side of the toxin B pentamer inhibited neutralizing antibody binding to the laterally located epitopes, rendering some glycan-receptor binding sites that remained available for the toxin binding and endocytosis process, which is strikingly different from the counterpart antibodies recognizing the far side-located epitopes. These results highlight additional features of the toxin-antibody interactions and offer important insights into anti-toxin strategies.


  • Organizational Affiliation

    Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative pertussis-like toxin subunit
A, B, C, D, E
114Salmonella enterica subsp. enterica serovar TyphiMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q8Z6A3 (Salmonella typhi)
Explore Q8Z6A3 
Go to UniProtKB:  Q8Z6A3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Z6A3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Light Chain Variable DomainF [auth L],
H [auth K],
J [auth N],
L [auth Q],
N [auth Y]
108Mus musculusMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Heavy Chain Variable DomainG [auth H],
I [auth J],
K [auth M],
M [auth P],
O [auth X]
119Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16-3549
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR03 AI135767
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM098621
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM116942

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Database references