› 6mss

X-ray diffraction
3Å resolution

Diversity in the type II Natural Killer T cell receptor repertoire and antigen specificity leads to differing CD1d docking strategies

Released:
DOI: 10.2210/pdb6mss/pdb
PDB entry 6mss coloured by chain, front view.
PDB entry 6mss coloured by chain, side view.
PDB entry 6mss coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Distinct CD1d docking strategies exhibited by diverse Type II NKT cell receptors.
Almeida CF, Sundararaj S, Le Nours J, Praveena T, Cao B, Burugupalli S, Smith DGM, Patel O, Brigl M, Pellicci DG, Williams SJ, Uldrich AP, Godfrey DI, Rossjohn J
Nat Commun 10 5242 (2019)
PMID: 31748533

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-208717 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
A11B8.2 NKT TCR alpha-chain Chain: A
Molecule details ›
Chain: A
Length: 203 amino acids
Theoretical weight: 22.64 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
A11B8.2 NKT TCR beta-chain Chain: B
Molecule details ›
Chain: B
Length: 245 amino acids
Theoretical weight: 27.41 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Antigen-presenting glycoprotein CD1d1 Chain: C
Molecule details ›
Chain: C
Length: 302 amino acids
Theoretical weight: 34.66 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P11609 (Residues: 19-297; Coverage: 88%)
Gene names: Cd1.1, Cd1d1
Sequence domains:
Beta-2-microglobulin Chain: D
Molecule details ›
Chain: D
Length: 99 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 2 x NAG
Ligand SRV 1 x SRV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P212121
Unit cell:
a: 42.58Å b: 141.26Å c: 170.67Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.183 0.242
Expression system: Escherichia coli

Quick links

Citations

3 review citations

NKT Cells Contribute to the Control of Microbial Infections.
Vogt et al. (2021)
2 more