PDBsum entry 5vu0

Immune system

PDB id: 5vu0

Contents

Protein chains

215 a.a.

165 a.a.

Ligands

NAG-NAG-BMA-MAN-NAG-GAL-MAN-NAG ×2

EDO ×5

PEG ×4

NAG ×2

Metals

_NA ×9

Waters ×254

PDB id:

5vu0

Name:

Immune system

Title:

Crystal structure of the complex between afucosylated/galactosylated human igg1 fc and fc gamma receptor iiia (cd16a) with man5 n-glycans

Structure:

Immunoglobulin gamma-1 heavy chain. Chain: a, b. Fragment: fc region (unp residues 230-446). Synonym: immunoglobulin gamma-1 heavy chain nie. Engineered: yes. Low affinity immunoglobulin gamma fc region receptor iii-a. Chain: c. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek 293-f. Gene: fcgr3a. Expression_system_cell_line: hek 293-f

Resolution:

2.26Å R-factor: 0.194 R-free: 0.237

Authors:

G.S.Subedi,A.M.Marcella,A.W.Barb

Key ref:

D.J.Falconer et al. (2018). Antibody Fucosylation Lowers the FcγRIIIa/CD16a Affinity by Limiting the Conformations Sampled by the N162-Glycan. ACS Chem Biol, 13, 2179-2189. PubMed id: 30016589 DOI: 10.1021/acschembio.8b00342

Date:

18-May-17 Release date: 23-May-18

Protein chains

P0DOX5  (IGG1_HUMAN) -  Immunoglobulin gamma-1 heavy chain from Homo sapiens

Seq: 449 a.a.

Struc: 215 a.a.

Protein chain

P08637  (FCG3A_HUMAN) -  Low affinity immunoglobulin gamma Fc region receptor III-A from Homo sapiens

Seq: 254 a.a.

Struc: 165 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DOI no: 10.1021/acschembio.8b00342

ACS Chem Biol 13:2179-2189 (2018)

PubMed id: 30016589

Antibody Fucosylation Lowers the FcγRIIIa/CD16a Affinity by Limiting the Conformations Sampled by the N162-Glycan.

D.J.Falconer, G.P.Subedi, A.M.Marcella, A.W.Barb.

ABSTRACT

Therapeutic monoclonal antibodies (mAbs) are largely based on the immunoglobulin G1 (IgG1) scaffold, and many elicit a cytotoxic cell-mediated response by binding Fc γ receptors. Core fucosylation, a prevalent modification to the asparagine (N)-linked carbohydrate on the IgG1 crystallizable fragment (Fc), decreases the Fc γ receptor IIIa (CD16a) binding affinity and mAb efficacy. We determined IgG1 Fc fucosylation reduced the CD16a affinity by 1.7 ± 0.1 kcal/mol when compared to that of afucosylated IgG1 Fc; however, CD16a N-glycan truncation decreased this penalty by 1.2 ± 0.1 kcal/mol or 70%. Fc fucosylation restricted the manifold of conformations sampled by displacing the CD16a Asn162-glycan that impinges upon the linkage between the α-mannose(1-6)β-mannose residues and promoted contacts with the IgG Tyr296 residue. Fucosylation also impacted the IgG1 Fc structure as indicated by changes in resonance frequencies and nuclear spin relaxation observed by solution nuclear magnetic resonance spectroscopy. The effects of fucosylation on IgG1 Fc may account for the remaining 0.5 ± 0.1 kcal/mol penalty of fucosylated IgG1 Fc binding CD16a when compared to that of afucosylated IgG1 Fc. Our results indicated the CD16a Asn162-glycan modulates the antibody affinity indirectly by reducing the volume sampled, as opposed to a direct mechanism with intermolecular glycan-glycan contacts previously proposed to stabilize this system. Thus, antibody engineering to enhance intermolecular glycan-glycan contacts will likely provide limited improvement, and future designs should maximize the affinity by maintaining the CD16a Asn162-glycan conformational heterogeneity.