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Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule

X-ray diffraction
2.41Å resolution
PDB entry 2icw coloured by chain, front view.
PDB entry 2icw coloured by chain, side view.
PDB entry 2icw coloured by chain, top view.
Source organisms:
Assembly composition:
hetero hexamer (preferred)
Entry contents: 6 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero hexamer
Accessible surface area: 36106.96 Å2
Buried surface area: 13759.03 Å2
Dissociation area: 2,216.1 Å2
Dissociation energy (ΔGdiss): 2.02 kcal/mol
Dissociation entropy (TΔSdiss): 24.36 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-106902
Assembly 2
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Multimeric state: hetero hexamer
Accessible surface area: 35960.0 Å2
Buried surface area: 13819.94 Å2
Dissociation area: 1,079.83 Å2
Dissociation energy (ΔGdiss): -0.95 kcal/mol
Dissociation entropy (TΔSdiss): 13.89 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-106902

Macromolecules

HLA class II histocompatibility antigen, DR alpha chain
Chains: A, D
Length: 179 amino acids
Theoretical weight: 20.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01903 (Residues: 28-206; Coverage: 78%)
Gene names: HLA-DRA, HLA-DRA1
Pfam:
InterPro:
CATH:
SCOP:
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 2icw, assembly 1, front view.
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 2icw, assembly 1, side view.
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 2icw, assembly 1, top view.
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HLA class II histocompatibility antigen, DRB1 beta chain
Chains: B, E
Length: 190 amino acids
Theoretical weight: 22.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01911 (Residues: 30-219; Coverage: 80%)
Gene name: HLA-DRB1
Pfam:
InterPro:
CATH:
SCOP:
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 2icw, assembly 1, front view.
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 2icw, assembly 1, side view.
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 2icw, assembly 1, top view.
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haemagglutinin peptide
Chains: C, F
Length: 13 amino acids
Theoretical weight: 1.51 KDa
haemagglutinin peptide in PDB entry 2icw, assembly 1, front view.
haemagglutinin peptide in PDB entry 2icw, assembly 1, side view.
haemagglutinin peptide in PDB entry 2icw, assembly 1, top view.
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Superantigen
Chains: G, H
Length: 213 amino acids
Theoretical weight: 25.33 KDa
Source organism: Metamycoplasma arthritidis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q48898 (Residues: 26-238; Coverage: 90%)
Pfam: Mycoplasma arthritidis-derived mitogen
InterPro:
CATH:
SCOP: Superantigen MAM
Superantigen in PDB entry 2icw, assembly 1, front view.
Superantigen in PDB entry 2icw, assembly 1, side view.
Superantigen in PDB entry 2icw, assembly 1, top view.
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T-cell receptor alpha chain V region PHDS58
Chains: I, K
Length: 110 amino acids
Theoretical weight: 12.11 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01738 (Residues: 21-130; Coverage: 100%)
Pfam: Immunoglobulin V-set domain
InterPro:
CATH: Immunoglobulins
T-cell receptor alpha chain V region PHDS58 in PDB entry 2icw, assembly 1, front view.
T-cell receptor alpha chain V region PHDS58 in PDB entry 2icw, assembly 1, side view.
T-cell receptor alpha chain V region PHDS58 in PDB entry 2icw, assembly 1, top view.
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Ig-like domain-containing protein
Chains: J, L
Length: 113 amino acids
Theoretical weight: 12.18 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A2NTY6 (Residues: 30-144; Coverage: 96%)
Pfam: Immunoglobulin V-set domain
InterPro:
CATH: Immunoglobulins
SCOP: V set domains (antibody variable domain-like)
Ig-like domain-containing protein in PDB entry 2icw, assembly 1, front view.
Ig-like domain-containing protein in PDB entry 2icw, assembly 1, side view.
Ig-like domain-containing protein in PDB entry 2icw, assembly 1, top view.
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