5YC5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered Fc gamma Receptor IIIa-Immobilized Column.

Kiyoshi, M.Caaveiro, J.M.M.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.

(2018) Sci Rep 8: 3955-3955

  • DOI: 10.1038/s41598-018-22199-8

  • PubMed Abstract: 
  • The N-glycan moiety of IgG-Fc has a significant impact on multifaceted properties of antibodies such as in their effector function, structure, and stability. Numerous studies have been devoted to understanding its biological effect since the exact co ...

    The N-glycan moiety of IgG-Fc has a significant impact on multifaceted properties of antibodies such as in their effector function, structure, and stability. Numerous studies have been devoted to understanding its biological effect since the exact composition of the Fc N-glycan modulates the magnitude of effector functions such as the antibody-dependent cell mediated cytotoxicity (ADCC), and the complement-dependent cytotoxicity (CDC). To date, systematic analyses of the properties and influence of glycan variants have been of great interest. Understanding the principles on how N-glycosylation modulates those properties is important for the molecular design, manufacturing, process optimization, and quality control of therapeutic antibodies. In this study, we have separated a model therapeutic antibody into three fractions according to the composition of the N-glycan by using a novel FcγRIIIa chromatography column. Notably, Fc galactosylation was a major factor influencing the affinity of IgG-Fc to the FcγRIIIa immobilized on the column. Each antibody fraction was employed for structural, biological, and physicochemical analysis, illustrating the mechanism by which galactose modulates the affinity to FcγRIIIa. In addition, we discuss the benefits of the FcγRIIIa chromatography column to assess the heterogeneity of the N-glycan.


    Organizational Affiliation

    Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, 158-8501, Japan. m.kiyoshi@nihs.go.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin gamma-1 heavy chain
A, B
223Homo sapiensMutation(s): 0 
Find proteins for P0DOX5 (Homo sapiens)
Go to UniProtKB:  P0DOX5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Low affinity immunoglobulin gamma Fc region receptor III-A
C
182Homo sapiensMutation(s): 9 
Gene Names: FCGR3A (CD16A, FCG3, FCGR3, IGFR3)
Find proteins for P08637 (Homo sapiens)
Go to Gene View: FCGR3A
Go to UniProtKB:  P08637
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.790α = 90.00
b = 101.420β = 90.00
c = 122.600γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan25249115
Japan Agency for Medical Research and Development (AMED)JapanResearch on Regulatory Science of 427 Pharmaceuticals and Medical Devices
Japan Society for the Promotion of ScienceJapan15K06962

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-07-04
    Type: Data collection, Database references