7K7H

Density-fitted Model Structure of Antibody Variable Domains of TyTx1 in Complex with PltB pentamer of Typhoid Toxin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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
Pertussis like toxin subunit B
A, B, C, D, E
114Salmonella enterica subsp. enterica serovar Typhi str. CT18Mutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q8Z6A3 (Salmonella typhi)
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Go to UniProtKB:  Q8Z6A3
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UniProt GroupQ8Z6A3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Light Chain Variable DomainF [auth L]114Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Heavy Chain Variable DomainG [auth H]118Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis toxin-like subunit ArtAH [auth G]14Salmonella enterica subsp. enterica serovar Typhi str. CT18Mutation(s): 0 
Gene Names: 
UniProt
Find proteins for A0A4Z0MXD9 (Salmonella enterica subsp. enterica serovar Poona)
Explore A0A4Z0MXD9 
Go to UniProtKB:  A0A4Z0MXD9
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UniProt GroupA0A4Z0MXD9
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16-3549
RECONSTRUCTIONRELION3

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 Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 GM098621
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)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