› 3o8x

X-ray diffraction
2.74Å resolution

Recognition of Glycolipid Antigen by iNKT Cell TCR

Released:
DOI: 10.2210/pdb3o8x/pdb
PDB entry 3o8x coloured by chain, front view.
PDB entry 3o8x coloured by chain, side view.
PDB entry 3o8x coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
The Vα14 invariant natural killer T cell TCR forces microbial glycolipids and CD1d into a conserved binding mode.
Li Y, Girardi E, Wang J, Yu ED, Painter GF, Kronenberg M, Zajonc DM
J Exp Med 207 2383-93 (2010)
PMID: 20921281

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-105336 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
Antigen-presenting glycoprotein CD1d1 Chain: A
Molecule details ›
Chain: A
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 Chain: B
Molecule details ›
Chain: B
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
T cell receptor alpha chain constant Chain: C
Molecule details ›
Chain: C
Length: 209 amino acids
Theoretical weight: 23.06 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC
Sequence domains: Domain of unknown function (DUF1968)
Structure domains: Immunoglobulins
T cell receptor beta constant 2 Chain: D
Molecule details ›
Chain: D
Length: 241 amino acids
Theoretical weight: 27.03 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A5B9 (Residues: 1-128; Coverage: 72%)
Gene names: TCRBC2, TRBC2
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
2 bound ligands:
Ligand GSL 1 x GSL
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: C2221
Unit cell:
a: 79Å b: 191.2Å c: 151.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.195 0.253
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)

Quick links

Citations

26 review citations

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

6 mentions without citation

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