3sdx

X-ray diffraction
3.12Å resolution

Crystal structure of human autoreactive-Valpha24 NKT TCR in complex with CD1d-beta-galactosylceramide

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-208593 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Antigen-presenting glycoprotein CD1d Chains: A, C
Molecule details ›
Chains: A, C
Length: 275 amino acids
Theoretical weight: 31.34 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P15813 (Residues: 24-295; Coverage: 86%)
Gene name: CD1D
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
Length: 99 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
T cell receptor alpha chain constant Chains: E, G
Molecule details ›
Chains: E, G
Length: 204 amino acids
Theoretical weight: 22.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01848 (Residues: 1-90; Coverage: 64%)
Gene names: TCRA, TRAC
Sequence domains: Domain of unknown function (DUF1968)
Structure domains: Immunoglobulins
NKT TCR autoreactive-Vbeta11 chain Chains: F, H
Molecule details ›
Chains: F, H
Length: 247 amino acids
Theoretical weight: 28.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: C2
Unit cell:
a: 209.041Å b: 152.337Å c: 85.119Å
α: 90° β: 97.24° γ: 90°
R-values:
R R work R free
0.234 0.232 0.273
Expression systems:
  • Trichoplusia ni
  • Escherichia coli