› 3vwk

X-ray diffraction
2.94Å resolution

Ternary crystal structure of the human NKT TCR-CD1d-4'deoxy-alpha-galactosylceramide complex

Released:
DOI: 10.2210/pdb3vwk/pdb
PDB entry 3vwk coloured by chain, front view.
PDB entry 3vwk coloured by chain, side view.
PDB entry 3vwk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Human and mouse type I natural killer T cell antigen receptors exhibit different fine specificities for CD1d-antigen complex.
Wun KS, Ross F, Patel O, Besra GS, Porcelli SA, Richardson SK, Keshipeddy S, Howell AR, Godfrey DI, Rossjohn J
J Biol Chem 287 39139-48 (2012)
PMID: 22995911

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-235071 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Antigen-presenting glycoprotein CD1d Chain: A
Molecule details ›
Chain: A
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:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
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 Chain: C
Molecule details ›
Chain: C
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 Chain: D
Molecule details ›
Chain: D
Length: 246 amino acids
Theoretical weight: 28.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

3 bound ligands:
Ligand NAG 2 x NAG
Ligand 4GH 1 x 4GH
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: C222
Unit cell:
a: 144.27Å b: 177.26Å c: 83.75Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.191 0.25
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

14 review citations

T cell antigen receptor recognition of antigen-presenting molecules.
Rossjohn et al. (2015)
13 more

3 mentions without citation

The T cell antigen receptor: the Swiss army knife of the immune system.
Attaf et al. (2015)
2 more