› 3qi9

X-ray diffraction
2.3Å resolution

Crystal structure of mouse CD1d-alpha-phosphotidylinositol with mouse Valpha14-Vbeta6 2A3-D NKT TCR

Released:
DOI: 10.2210/pdb3qi9/pdb
PDB entry 3qi9 coloured by chain, front view.
PDB entry 3qi9 coloured by chain, side view.
PDB entry 3qi9 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
A molecular basis for NKT cell recognition of CD1d-self-antigen.
Mallevaey T, Clarke AJ, Scott-Browne JP, Young MH, Roisman LC, Pellicci DG, Patel O, Vivian JP, Matsuda JL, McCluskey J, Godfrey DI, Marrack P, Rossjohn J, Gapin L
Immunity 34 315-26 (2011)
PMID: 21376640

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-233904 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Antigen-presenting glycoprotein CD1d1 Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 34.66 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
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: Trichoplusia ni
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
NKT TCR V alpha 14 Chain: C
Molecule details ›
Chain: C
Length: 207 amino acids
Theoretical weight: 22.78 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins
NKT TCR V beta 6 2A3-D Chain: D
Molecule details ›
Chain: D
Length: 243 amino acids
Theoretical weight: 27.32 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
4 bound ligands:
Ligand NAG 2 x NAG
Ligand PII 1 x PII
Ligand MG 1 x MG
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P41212
Unit cell:
a: 95.697Å b: 95.697Å c: 289.71Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.248 0.247 0.275
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

45 review citations

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

3 mentions without citation

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