› 3u0p

X-ray diffraction
2.8Å resolution

Crystal structure of human CD1d-lysophosphatidylcholine

Released:
DOI: 10.2210/pdb3u0p/pdb
PDB entry 3u0p coloured by chain, front view.
PDB entry 3u0p coloured by chain, side view.
PDB entry 3u0p 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

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147491 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (5 distinct):
Antigen-presenting glycoprotein CD1d Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 284 amino acids
Theoretical weight: 32.41 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 Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 102 amino acids
Theoretical weight: 12.03 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
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
6 bound ligands:
Ligand LSC 2 x LSC
Ligand HEX 1 x HEX
Ligand SO4 11 x SO4
Ligand GOL 7 x GOL
Ligand UND 1 x UND
Ligand NBU 1 x NBU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: I222
Unit cell:
a: 108.609Å b: 127.189Å c: 332.641Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.213 0.259
Expression system: Trichoplusia ni

Quick links

Citations

21 review citations

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

5 mentions without citation

Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor.
López-Sagaseta et al. (2012)
4 more