› 4en3

X-ray diffraction
2.57Å resolution

Crystal structure of a human Valpha24(-) NKT TCR in complex with CD1d/alpha-galactosylceramide

Released:
DOI: 10.2210/pdb4en3/pdb
PDB entry 4en3 coloured by chain, front view.
PDB entry 4en3 coloured by chain, side view.
PDB entry 4en3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The molecular basis for recognition of CD1d/α-galactosylceramide by a human non-Vα24 T cell receptor.
López-Sagaseta J, Kung JE, Savage PB, Gumperz J, Adams EJ
PLoS Biol 10 e1001412 (2012)
PMID: 23109910

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-125596 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Antigen-presenting glycoprotein CD1d Chain: C
Molecule details ›
Chain: C
Length: 284 amino acids
Theoretical weight: 32.37 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P15813 (Residues: 21-295; Coverage: 87%)
Gene name: CD1D
Sequence domains:
Structure domains:
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 220 amino acids
Theoretical weight: 24.52 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: K7N5M3 (Residues: 1-220; Coverage: 100%)
Gene names: B2M, HDCMA22P
Sequence domains:
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 259 amino acids
Theoretical weight: 29.32 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: K7N5M4 (Residues: 1-259; Coverage: 100%)
Gene names: B2M, HDCMA22P
Sequence domains:
Structure domains: Immunoglobulins
Beta-2-microglobulin Chain: D
Molecule details ›
Chain: D
Length: 100 amino acids
Theoretical weight: 11.85 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

Ligands and Environments

4 bound ligands:
Ligand NAG 5 x NAG
Ligand AGH 1 x AGH
Ligand FUC 1 x FUC
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21
Unit cell:
a: 57.112Å b: 72.573Å c: 113.747Å
α: 90° β: 103.31° γ: 90°
R-values:
R R work R free
0.211 0.208 0.266
Expression system: Trichoplusia ni

Quick links

Citations

7 review citations

Invariant natural killer T cells: an innate activation scheme linked to diverse effector functions.
Brennan et al. (2013)
6 more

9 mentions without citation

Recognition of CD1d-restricted antigens by natural killer T cells.
Rossjohn et al. (2012)
8 more