4P2C image
Deposition Date 2014-03-03
Release Date 2014-07-30
Last Version Date 2024-10-30
Entry Detail
PDB ID:
4P2C
Keywords:
Title:
Complex of Shiga toxin 2e with a neutralizing single-domain antibody
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Lama glama (Taxon ID: 9844)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.82 Å
R-Value Free:
0.25
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Shiga toxin 2e, subunit A
Mutagens:Y99S, E189Q, K296T, P313S
Chain IDs:A
Chain Length:297
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Shiga toxin 2e, subunit B
Gene (Uniprot):stx2e B
Chain IDs:B, C, D, E, F
Chain Length:68
Number of Molecules:5
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nanobody 1, Anti-F4+ETEC bacteria VHH variable region
Chain IDs:G, H, I, J, K
Chain Length:128
Number of Molecules:5
Biological Source:Lama glama
Ligand Molecules
Primary Citation
The Molecular Mechanism of Shiga Toxin Stx2e Neutralization by a Single-domain Antibody Targeting the Cell Receptor-binding Domain.
J.Biol.Chem. 289 25374 25381 (2014)
PMID: 25053417 DOI: 10.1074/jbc.M114.566257

Abstact

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.

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Protein

Chemical

Disease

Primary Citation of related structures