› 6cxe

X-ray diffraction
2.05Å resolution

Structure of alpha-GSA[26,6P] bound by CD1d and in complex with the Va14Vb8.2 TCR

Released:
DOI: 10.2210/pdb6cxe/pdb
PDB entry 6cxe coloured by chain, front view.
PDB entry 6cxe coloured by chain, side view.
PDB entry 6cxe coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
A molecular switch in mouse CD1d modulates natural killer T cell activation by α-galactosylsphingamides.
Wang J, Guillaume J, Janssens J, Remesh SG, Ying G, Bitra A, Van Calenbergh S, Zajonc DM
J Biol Chem 294 14345-14356 (2019)
PMID: 31391251

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-238648 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Chimeric T cell antigen receptor alpha chain Va14,Va24,Ja18 Chain: C
Molecule details ›
Chain: C
Length: 209 amino acids
Theoretical weight: 23.06 KDa
Source organism: Mus musculus
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Structure domains: Immunoglobulins
Chimeric T cell antigen receptor beta chain Vb8.2, vb11 Chain: D
Molecule details ›
Chain: D
Length: 241 amino acids
Theoretical weight: 27.03 KDa
Source organism: Mus musculus
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Structure domains: Immunoglobulins
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

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
3 bound ligands:
Ligand NA 4 x NA
Ligand NAG 2 x NAG
Ligand EM4 1 x EM4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: C2221
Unit cell:
a: 78.437Å b: 189.071Å c: 150.908Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.209 0.248
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Spodoptera frugiperda

Quick links

Citations

1 mention without citation

A molecular switch in mouse CD1d modulates natural killer T cell activation by α-galactosylsphingamides.
Wang et al. (2019)