› 4c56

X-ray diffraction
2.9Å resolution

X-ray structure of the complex between staphylococcal enterotoxin B, T cell receptor and major histocompatibility complex class II

Released:
DOI: 10.2210/pdb4c56/pdb
PDB entry 4c56 coloured by chain, front view.
PDB entry 4c56 coloured by chain, side view.
PDB entry 4c56 coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the superantigen staphylococcal enterotoxin B in complex with TCR and peptide-MHC demonstrates absence of TCR-peptide contacts.
Rödström KE, Elbing K, Lindkvist-Petersson K
J Immunol 193 1998-2004 (2014)
PMID: 25015819

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-498015 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
T cell receptor alpha chain constant Chains: A, G
Molecule details ›
Chains: A, G
Length: 206 amino acids
Theoretical weight: 22.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC
Sequence domains: Domain of unknown function (DUF1968)
Structure domains: Immunoglobulins
T cell receptor beta constant 2 Chains: B, H
Molecule details ›
Chains: B, H
Length: 244 amino acids
Theoretical weight: 27.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A5B9 (Residues: 1-129; Coverage: 73%)
Gene names: TCRBC2, TRBC2
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Enterotoxin type B Chains: C, I
Molecule details ›
Chains: C, I
Length: 238 amino acids
Theoretical weight: 28.28 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P01552 (Residues: 29-266; Coverage: 100%)
Gene name: entB
Sequence domains:
Structure domains:
HLA class II histocompatibility antigen, DR alpha chain Chains: D, J
Molecule details ›
Chains: D, J
Length: 182 amino acids
Theoretical weight: 21.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01903 (Residues: 26-207; Coverage: 80%)
Gene names: HLA-DRA, HLA-DRA1
Sequence domains:
Structure domains:
HLA class II histocompatibility antigen, DRB1 beta chain Chains: E, K
Molecule details ›
Chains: E, K
Length: 190 amino acids
Theoretical weight: 22.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01911 (Residues: 30-219; Coverage: 80%)
Gene name: HLA-DRB1
Sequence domains:
Structure domains:
Hemagglutinin HA1 chain Chains: F, L
Molecule details ›
Chains: F, L
Length: 13 amino acids
Theoretical weight: 1.51 KDa
Source organism: Influenza A virus
Expression system: Not provided
UniProt:
  • Canonical: P03437 (Residues: 322-334; Coverage: 2%)
Gene name: HA

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P21
Unit cell:
a: 66.35Å b: 217.65Å c: 101.41Å
α: 90° β: 99.82° γ: 90°
R-values:
R R work R free
0.234 0.233 0.251
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli K-12
  • Not provided

Quick links

Citations

6 review citations

Staphylococcus aureus Secreted Toxins and Extracellular Enzymes.
Tam et al. (2019)
5 more

15 mentions without citation

Superantigen Recognition and Interactions: Functions, Mechanisms and Applications.
Deacy et al. (2021)
14 more