› 3tzv

X-ray diffraction
3.06Å resolution

Crystal structure of an iNKT TCR in complex with CD1d-lysophosphatidylcholine

Released:
DOI: 10.2210/pdb3tzv/pdb
PDB entry 3tzv coloured by chain, front view.
PDB entry 3tzv coloured by chain, side view.
PDB entry 3tzv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor.
López-Sagaseta J, Sibener LV, Kung JE, Gumperz J, Adams EJ
EMBO J 31 2047-59 (2012)
PMID: 22395072

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
hetero dimer
PDBe Complex ID:
PDB-CPX-210657 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Invariant Natural Killer T Cell Receptor chain A Chains: A, G
Molecule details ›
Chains: A, G
Length: 213 amino acids
Theoretical weight: 23.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Invariant Natural Killer T Cell Receptor chain B Chains: B, H
Molecule details ›
Chains: B, H
Length: 259 amino acids
Theoretical weight: 29.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Antigen-presenting glycoprotein CD1d Chain: C
Molecule details ›
Chain: C
Length: 276 amino acids
Theoretical weight: 31.39 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P15813 (Residues: 21-295; Coverage: 87%)
Gene name: CD1D
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: D
Molecule details ›
Chain: D
Length: 99 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
4 bound ligands:
Ligand LSC 1 x LSC
Ligand HEX 1 x HEX
Ligand D12 1 x D12
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 66.591Å b: 117.605Å c: 190.656Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.239 0.236 0.288
Expression systems:
  • Escherichia coli
  • Trichoplusia ni

Quick links

Citations

20 review citations

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

5 mentions without citation

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