4P2C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.818 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 

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

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Shiga toxin 2e, subunit A
A
297Escherichia coliMutation(s): 2 
Find proteins for Q7WUF4 (Escherichia coli)
Go to UniProtKB:  Q7WUF4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Shiga toxin 2e, subunit B
B, C, D, E, F
68Escherichia coliMutation(s): 0 
Gene Names: stxB2e (orf, stx2e B, stx2eB, stxB)
Find proteins for Q47644 (Escherichia coli)
Go to UniProtKB:  Q47644
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nanobody 1, Anti-F4+ETEC bacteria VHH variable region
G, H, I, J, K
128Lama glamaMutation(s): 0 
Find proteins for R9VYW2 (Lama glama)
Go to UniProtKB:  R9VYW2
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.818 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 191.838α = 90.00
b = 88.192β = 90.00
c = 100.664γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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