› 3he6

X-ray diffraction
2.9Å resolution

Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta8.2 NKT TCR

Released:
DOI: 10.2210/pdb3he6/pdb
PDB entry 3he6 coloured by chain, front view.
PDB entry 3he6 coloured by chain, side view.
PDB entry 3he6 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors.
Pellicci DG, Patel O, Kjer-Nielsen L, Pang SS, Sullivan LC, Kyparissoudis K, Brooks AG, Reid HH, Gras S, Lucet IS, Koh R, Smyth MJ, Mallevaey T, Matsuda JL, Gapin L, McCluskey J, Godfrey DI, Rossjohn J
Immunity 31 47-59 (2009)
PMID: 19592275

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-233901 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Antigen-presenting glycoprotein CD1d1 Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 34.66 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P11609 (Residues: 19-297; Coverage: 88%)
Gene names: Cd1.1, Cd1d1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Valpha14(mouse variable domain, human constant domain) Chain: C
Molecule details ›
Chain: C
Length: 207 amino acids
Theoretical weight: 22.78 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins
T cell receptor beta constant 1 Chain: D
Molecule details ›
Chain: D
Length: 244 amino acids
Theoretical weight: 27.17 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01850 (Residues: 1-129; Coverage: 73%)
Gene name: TRBC1
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 2 x NAG
Ligand AGH 1 x AGH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P212121
Unit cell:
a: 61.113Å b: 81.506Å c: 233.451Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.234 0.298
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

43 review citations

Raising the NKT cell family.
Godfrey et al. (2010)
42 more

30 mentions without citation

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