› 8glh

X-ray diffraction
1.83Å resolution

Crystal Structure of Human CD1b in Complex with Endogenous PC C40:5

Released:
DOI: 10.2210/pdb8glh/pdb
PDB entry 8glh coloured by chain, front view.
PDB entry 8glh coloured by chain, side view.
PDB entry 8glh coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
CD1 lipidomes reveal lipid-binding motifs and size-based antigen-display mechanisms.
Huang S, Shahine A, Cheng TY, Chen YL, Ng SW, Balaji GR, Farquhar R, Gras S, Hardman CS, Altman JD, Tahiri N, Minnaard AJ, Ogg GS, Mayfield JA, Rossjohn J, Moody DB
Cell 186 4583-4596.e13 (2023)
PMID: 37725977

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

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:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 101 amino acids
Theoretical weight: 11.97 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

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, FUC
Carbohydrate polymer
5 bound ligands:
Ligand IOD 3 x IOD
Ligand 3IV 1 x 3IV
Ligand 3IY 1 x 3IY
Ligand EDO 4 x EDO
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: 57.447Å b: 77.049Å c: 91.445Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.166 0.221
Expression system: Trichoplusia ni

Quick links

Citations

2 review citations

CD1a and skin T cells: a pathway for therapeutic intervention.
Ye et al. (2024)
1 more