Salmonella Typhi PltB Homopentamer with Neu-5NAc-9OAc-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans

Experimental Data Snapshot

  • Resolution: 2.33 Å

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


The role of 9-O-acetylated glycan receptor moieties in the typhoid toxin binding and intoxication.

Nguyen, T.Lee, S.Yang, Y.A.Ahn, C.Sim, J.H.Kei, T.G.Barnard, K.N.Yu, H.Millano, S.K.Chen, X.Parrish, C.R.Song, J.

(2020) PLoS Pathog 16: e1008336-e1008336

  • DOI: https://doi.org/10.1371/journal.ppat.1008336
  • Primary Citation of Related Structures:  
    6TYN, 6TYO, 6TYQ

  • PubMed Abstract: 

    Typhoid toxin is an A2B5 toxin secreted from Salmonella Typhi-infected cells during human infection and is suggested to contribute to typhoid disease progression and the establishment of chronic infection. To deliver the enzymatic 'A' subunits of the toxin to the site of action in host cells, the receptor-binding 'B' subunit PltB binds to the trisaccharide glycan receptor moieties terminated in N-acetylneuraminic acid (Neu5Ac) that is α2-3 or α2-6 linked to the underlying disaccharide, galactose (Gal) and N-acetylglucosamine (GlcNAc). Neu5Ac is present in both unmodified and modified forms, with 9-O-acetylated Neu5Ac being the most common modification in humans. Here we show that host cells associated with typhoid toxin-mediated clinical signs express both unmodified and 9-O-acetylated glycan receptor moieties. We found that PltB binds to 9-O-acetylated α2-3 glycan receptor moieties with a markedly increased affinity, while the binding affinity to 9-O-acetylated α2-6 glycans is only slightly higher, as compared to the affinities of PltB to the unmodified counterparts, respectively. We also present X-ray co-crystal structures of PltB bound to related glycan moieties, which supports the different effects of 9-O-acetylated α2-3 and α2-6 glycan receptor moieties on the toxin binding. Lastly, we demonstrate that the cells exclusively expressing unmodified glycan receptor moieties are less susceptible to typhoid toxin than the cells expressing 9-O-acetylated counterparts, although typhoid toxin intoxicates both cells. These results reveal a fine-tuning mechanism of a bacterial toxin that exploits specific chemical modifications of its glycan receptor moieties for virulence and provide useful insights into the development of therapeutics against typhoid fever.

  • Organizational Affiliation

    Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis like toxin subunit B
A, B, C, D, E
114Salmonella enterica subsp. enterica serovar TyphiMutation(s): 0 
Gene Names: 
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
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, G, H, I, J
Glycosylation Resources
GlyTouCan:  G73077PR
GlyCosmos:  G73077PR
GlyGen:  G73077PR
Experimental Data & Validation

Experimental Data

  • Resolution: 2.33 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.675α = 90
b = 97.747β = 90
c = 101.452γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

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 StatesR01 AI137345
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI139625
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI141514
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR03 AI135767

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary