› 5yc5

X-ray diffraction
2.71Å resolution

Crystal structure of human IgG-Fc in complex with aglycan and optimized Fc gamma receptor IIIa

Released:
DOI: 10.2210/pdb5yc5/pdb
PDB entry 5yc5 coloured by chain, front view.
PDB entry 5yc5 coloured by chain, side view.
PDB entry 5yc5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column.
Kiyoshi M, Caaveiro JMM, Tada M, Tamura H, Tanaka T, Terao Y, Morante K, Harazono A, Hashii N, Shibata H, Kuroda D, Nagatoishi S, Oe S, Ide T, Tsumoto K, Ishii-Watabe A
Sci Rep 8 3955 (2018)
PMID: 29500371

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: 25.11 KDa
Source organism: Homo sapiens
Expression system: unidentified
UniProt:
  • Canonical: P0DOX5 (Residues: 226-448; 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: 182 amino acids
Theoretical weight: 20.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P08637 (Residues: 19-193; Coverage: 74%)
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, FUC
Carbohydrate polymer
1 bound ligand:
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 72.79Å b: 101.42Å c: 122.6Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.209 0.273
Expression systems:
  • unidentified
  • Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Monitoring of immunoglobulin N- and O-glycosylation in health and disease.
de Haan et al. (2020)
4 more

2 mentions without citation

Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column.
Kiyoshi et al. (2018)
1 more