› 5wke

X-ray diffraction
1.69Å resolution

Crystal Structure of Human CD1b in Complex with PS

Released:
DOI: 10.2210/pdb5wke/pdb
PDB entry 5wke coloured by chain, front view.
PDB entry 5wke coloured by chain, side view.
PDB entry 5wke coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A molecular basis of human T cell receptor autoreactivity toward self-phospholipids.
Shahine A, Van Rhijn I, Cheng TY, Iwany S, Gras S, Moody DB, Rossjohn J
Sci Immunol 2 (2017)
PMID: 29054999

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-151323 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
T-cell surface glycoprotein CD1b Chain: A
Molecule details ›
Chain: A
Length: 300 amino acids
Theoretical weight: 33.53 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P29016 (Residues: 20-296; Coverage: 88%)
Gene name: CD1B
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
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
Carbohydrate polymer : NEW Components: NAG, FUC, BMA, MAN
Carbohydrate polymer
6 bound ligands:
Ligand CUY 1 x CUY
Ligand NAG 1 x NAG
Ligand EDO 3 x EDO
Ligand CL 7 x CL
Ligand P50 1 x P50
Ligand NA 3 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P212121
Unit cell:
a: 57.25Å b: 78.55Å c: 84.79Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.239
Expression system: Trichoplusia ni

Quick links

Citations

8 review citations

Lipids hide or step aside for CD1-autoreactive T cell receptors.
Cotton et al. (2018)
7 more

4 mentions without citation

Novel Molecular Insights into Human Lipid-Mediated T Cell Immunity.
Shahine et al. (2021)
3 more