4P2C

Complex of Shiga toxin 2e with a neutralizing single-domain antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Molecular Mechanism of Shiga Toxin Stx2e Neutralization by a Single-domain Antibody Targeting the Cell Receptor-binding Domain.

Lo, A.W.Moonens, K.De Kerpel, M.Brys, L.Pardon, E.Remaut, H.De Greve, H.

(2014) J Biol Chem 289: 25374-25381

  • DOI: 10.1074/jbc.M114.566257
  • Primary Citation of Related Structures:  
    4P2C

  • PubMed Abstract: 
  • Shiga toxin Stx2e is the major known agent that causes edema disease in newly weaned pigs. This severe disease is characterized by neurological disorders, hemorrhagic lesions, and frequent fatal outcomes. Stx2e consists of an enzymatically active A s ...

    Shiga toxin Stx2e is the major known agent that causes edema disease in newly weaned pigs. This severe disease is characterized by neurological disorders, hemorrhagic lesions, and frequent fatal outcomes. Stx2e consists of an enzymatically active A subunit and five B subunits that bind to a specific glycolipid receptor on host cells. It is evident that antibodies binding to the A subunit or the B subunits of Shiga toxin variants may have the capability to inhibit their cytotoxicity. Here, we report the discovery and characterization of a VHH single domain antibody (nanobody) isolated from a llama phage display library that confers potent neutralizing capacity against Stx2e toxin. We further present the crystal structure of the complex formed between the nanobody (NbStx2e1) and the Stx2e toxoid, determined at 2.8 Å resolution. Structural analysis revealed that for each B subunit of Stx2e, one NbStx2e1 is interacting in a head-to-head orientation and directly competing with the glycolipid receptor binding site on the surface of the B subunit. The neutralizing NbStx2e1 can in the future be used to prevent or treat edema disease.


    Organizational Affiliation

    From Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Structural Biology Brussels, and hdegreve@vub.ac.be.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Shiga toxin 2e, subunit AA297Escherichia coliMutation(s): 4 
EC: 3.2.2.22
Find proteins for Q7WUF4 (Escherichia coli)
Explore Q7WUF4 
Go to UniProtKB:  Q7WUF4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Shiga toxin 2e, subunit BBCDEF68Escherichia coliMutation(s): 0 
Gene Names: 
Find proteins for Q47644 (Escherichia coli)
Explore Q47644 
Go to UniProtKB:  Q47644
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody 1, Anti-F4+ETEC bacteria VHH variable regionGHIJK128Lama glamaMutation(s): 0 
Find proteins for R9VYW2 (Lama glama)
Explore R9VYW2 
Go to UniProtKB:  R9VYW2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.838α = 90
b = 88.192β = 90
c = 100.664γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy