PDBe 3huj

X-ray diffraction
2.5Å resolution

Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant NKT cell receptor

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Antigen-presenting glycoprotein CD1d Chains: A, C
Molecule details ›
Chains: A, C
Length: 284 amino acids
Theoretical weight: 32.32 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P15813 (Residues: 21-295; Coverage: 87%)
Gene name: CD1D
Sequence domains: Immunoglobulin C1-set domain
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
NKT15 T cell receptor alpha-chain Chains: E, G
Molecule details ›
Chains: E, G
Length: 209 amino acids
Theoretical weight: 23.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
NKT15 T cell receptor beta-chain Chains: F, H
Molecule details ›
Chains: F, H
Length: 246 amino acids
Theoretical weight: 28.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments


No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P2
Unit cell:
a: 112.112Å b: 82.36Å c: 117.184Å
α: 90° β: 101.26° γ: 90°
R-values:
R R work R free
0.219 0.216 0.279
Expression systems:
  • Trichoplusia ni
  • Escherichia coli