› 6cwb

X-ray diffraction
2.85Å resolution

Structure of alpha-GSA[8,4P] bound by CD1d and in complex with the Va14Vb8.2 TCR

Released:
DOI: 10.2210/pdb6cwb/pdb
Model geometry
Fit model/data
PDB entry 6cwb coloured by chain, front view.
PDB entry 6cwb coloured by chain, side view.
PDB entry 6cwb 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-230733 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 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
Chimeric T cell antigen receptor alpha chain Va14,Va24,Ja18 Chain: C
Chimeric T cell antigen receptor beta chain Vb8.2, vb11 Chain: D

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: C2221
Unit cell:
a: 78.31Å b: 190.269Å c: 151.018Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.215 0.275
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

1 citations in other articles

A Humanized Mouse Model Coupled with Computational Analysis Identifies Potent Glycolipid Agonist of Invariant NKT Cells.
Saavedra-Avila et al. (2024)

1 mention without citation

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