› 4elm

X-ray diffraction
3.48Å resolution

Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex

Released:
DOI: 10.2210/pdb4elm/pdb
PDB entry 4elm coloured by chain, front view.
PDB entry 4elm coloured by chain, side view.
PDB entry 4elm coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Type II natural killer T cells use features of both innate-like and conventional T cells to recognize sulfatide self antigens.
Girardi E, Maricic I, Wang J, Mac TT, Iyer P, Kumar V, Zajonc DM
Nat Immunol 13 851-6 (2012)
PMID: 22820602

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-208704 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
Antigen-presenting glycoprotein CD1d1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 285 amino acids
Theoretical weight: 32.63 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P11609 (Residues: 19-297; Coverage: 88%)
Gene names: Cd1.1, Cd1d1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
Length: 99 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Hy19.3 TCR alpha chain (mouse variable domain, human constant domain) Chains: E, G
Molecule details ›
Chains: E, G
Length: 208 amino acids
Theoretical weight: 23.21 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
Structure domains: Immunoglobulins
Hy19.3 TCR beta chain (mouse variable domain, human constant domain) Chains: F, H
Molecule details ›
Chains: F, H
Length: 244 amino acids
Theoretical weight: 27.99 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, FUC
Carbohydrate polymer
3 bound ligands:
Ligand NAG 4 x NAG
Ligand SGF 2 x SGF
Ligand PLM 2 x PLM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P21
Unit cell:
a: 98.514Å b: 126.996Å c: 104.349Å
α: 90° β: 110.53° γ: 90°
R-values:
R R work R free
0.212 0.209 0.265
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)

Quick links

Citations

50 review citations

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

5 mentions without citation

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