› 5wkg

X-ray diffraction
2.06Å resolution

Crystal Structure of Human CD1b in Complex with PA

Released:
DOI: 10.2210/pdb5wkg/pdb
PDB entry 5wkg coloured by chain, front view.
PDB entry 5wkg coloured by chain, side view.
PDB entry 5wkg 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, BMA, MAN, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
8 bound ligands:
Ligand NAG 1 x NAG
Ligand D21 1 x D21
Ligand CUY 1 x CUY
Ligand PEG 1 x PEG
Ligand CL 4 x CL
Ligand EDO 1 x EDO
Ligand IOD 3 x IOD
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P212121
Unit cell:
a: 57.19Å b: 78.53Å c: 84.71Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.171 0.224
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

3 mentions without citation

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