› 6mja

X-ray diffraction
2.35Å resolution

Crystal structure of the mCD1d/xxo (JJ294) /iNKTCR ternary complex

Released:
DOI: 10.2210/pdb6mja/pdb
PDB entry 6mja coloured by chain, front view.
PDB entry 6mja coloured by chain, side view.
PDB entry 6mja coloured by chain, top view.
Source organisms:
Primary publication:
4"-O-Alkylated α-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies.
Janssens J, Bitra A, Wang J, Decruy T, Venken K, van der Eycken J, Elewaut D, Zajonc DM, van Calenbergh S
ChemMedChem 14 147-168 (2019)
PMID: 30556652

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-100911 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
Ig-like domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 209 amino acids
Theoretical weight: 23.06 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: K7N5M3 (Residues: 3-3, 96-114, 116-210; Coverage: 52%)
  • Canonical: A0A0B4J1J9 (Residues: 22-114; Coverage: 100%)
Gene names: B2M, HDCMA22P, Trav11, Trav11d
Sequence domains:
Structure domains: Immunoglobulins
Ig-like domain-containing protein; T cell receptor beta constant 2 Chain: D
Molecule details ›
Chain: D
Length: 241 amino acids
Theoretical weight: 27.03 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A2NTY6 (Residues: 29-123, 132-144; Coverage: 93%)
  • Canonical: A0N8J3 (Residues: 109-126, 128-129; Coverage: 7%)
  • Canonical: A0A5B9 (Residues: 21-128; Coverage: 61%)
Gene names: TCRBC2, TRBC2
Sequence domains:
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
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, FUC
Carbohydrate polymer
4 bound ligands:
Ligand NA 2 x NA
Ligand GOL 3 x GOL
Ligand NAG 1 x NAG
Ligand JTJ 1 x JTJ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: C2221
Unit cell:
a: 79.037Å b: 191.486Å c: 151.131Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.237
Expression systems:
  • Escherichia coli BL21(DE3)
  • Spodoptera frugiperda

Quick links

Citations

1 review citation

Natural and synthetic carbohydrate-based vaccine adjuvants and their mechanisms of action.
Pifferi et al. (2021)
6 other articles