› 5xjf

X-ray diffraction
2.5Å resolution

Crystal structure of fucosylated IgG Fc Y296W mutant complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa

Released:
DOI: 10.2210/pdb5xjf/pdb
PDB entry 5xjf coloured by chain, front view.
PDB entry 5xjf coloured by chain, side view.
PDB entry 5xjf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa.
Sakae Y, Satoh T, Yagi H, Yanaka S, Yamaguchi T, Isoda Y, Iida S, Okamoto Y, Kato K
Sci Rep 7 13780 (2017)
PMID: 29062024

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140253 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Immunoglobulin gamma-1 heavy chain Chains: A, B
Molecule details ›
Chains: A, B
Length: 223 amino acids
Theoretical weight: 25.12 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P0DOX5 (Residues: 227-449; Coverage: 50%)
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Low affinity immunoglobulin gamma Fc region receptor III-A Chain: C
Molecule details ›
Chain: C
Length: 179 amino acids
Theoretical weight: 20.64 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P08637 (Residues: 21-193; Coverage: 73%)
Gene names: CD16A, FCG3, FCGR3, FCGR3A, IGFR3
Sequence domains: Immunoglobulin domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN, GAL, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
2 bound ligands:
Ligand CL 1 x CL
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P41212
Unit cell:
a: 77.3Å b: 77.3Å c: 349.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.22 0.27
Expression system: Cricetulus griseus

Quick links

Citations

11 review citations

The recognition of glycans by protein receptors. Insights from NMR spectroscopy.
Ardá et al. (2018)
10 more

2 mentions without citation

Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa.
Sakae et al. (2017)
1 more