› 3w2d

X-ray diffraction
3.1Å resolution

Crystal Structure of Staphylococcal Eenterotoxin B in complex with a novel neutralization monoclonal antibody Fab fragment

Released:
DOI: 10.2210/pdb3w2d/pdb
PDB entry 3w2d coloured by chain, front view.
PDB entry 3w2d coloured by chain, side view.
PDB entry 3w2d coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for the neutralization and specificity of Staphylococcal enterotoxin B against its MHC Class II binding site.
Xia T, Liang S, Wang H, Hu S, Sun Y, Yu X, Han J, Li J, Guo S, Dai J, Lou Z, Guo Y
MAbs 6 119-29
PMID: 24423621

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208432 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Enterotoxin type B Chain: A
Molecule details ›
Chain: A
Length: 239 amino acids
Theoretical weight: 28.41 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01552 (Residues: 28-266; Coverage: 100%)
Gene name: entB
Sequence domains:
Structure domains:
Monoclonal Antibody 3E2 Fab figment light chain Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.46 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Monoclonal Antibody 3E2 Fab figment heavy chain Chain: H
Molecule details ›
Chain: H
Length: 223 amino acids
Theoretical weight: 24.44 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P2
Unit cell:
a: 40.561Å b: 109.308Å c: 86.222Å
α: 90° β: 96.08° γ: 90°
R-values:
R R work R free
0.2 0.196 0.261
Expression system: Escherichia coli

Quick links

Citations

6 citation in other articles

Isotype switching increases efficacy of antibody protection against staphylococcal enterotoxin B-induced lethal shock and Staphylococcus aureus sepsis in mice.
Varshney et al. (2014)
5 more

3 mentions without citation

Co-optimization of therapeutic antibody affinity and specificity using machine learning models that generalize to novel mutational space.
Makowski et al. (2022)
2 more