5YC5 | pdb_00005yc5

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

• PDB DOI: https://doi.org/10.2210/pdb5YC5/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: unidentified, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-09-06 Released: 2018-03-21 
• Deposition Author(s): Caaveiro, J.M.M., Tamura, H., Tsumoto, K., Kiyoshi, M.
• Funding Organization(s): Japan Society for the Promotion of Science, Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.273 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

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

• PubMed: 29500371 
• DOI: https://doi.org/10.1038/s41598-018-22199-8
• Primary Citation Related Structures: 
  5YC5


• 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 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.

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Organizational Affiliation: 
• Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, 158-8501, Japan. [e-mail].
Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
Graduate school of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Tokyo, 158-8501, Japan.
Tosoh Corporation, Hayakawa, Ayase, Kanagawa, 252-1123, Japan.
Institute of Medical Sciences, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
Laboratory of Pharmacokinetic Optimization, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki City, Osaka, 567-0085, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 74.06 kDa 
• Atom Count: 4,995 
• Modeled Residue Count: 595 
• Deposited Residue Count: 628 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin gamma-1 heavy chain	A, B	223	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Low affinity immunoglobulin gamma Fc region receptor III-A	C	182	Homo sapiens	Mutation(s): 10  Gene Names: FCGR3A, CD16A, FCG3, FCGR3, IGFR3
UniProt & NIH Common Fund Data Resources
Find proteins for P08637 (Homo sapiens) Explore P08637  Go to UniProtKB:  P08637
PHAROS:  P08637 GTEx:  ENSG00000203747

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	9		N-Glycosylation
Glycosylation Resources
GlyTouCan: G27919IH GlyCosmos: G27919IH GlyGen: G27919IH

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G80858MF GlyCosmos: G80858MF GlyGen: G80858MF

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.273 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.79	α = 90
b = 101.42	β = 90
c = 122.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Caaveiro, J.M.M., Tamura, H., Tsumoto, K., Kiyoshi, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	25249115
Japan Agency for Medical Research and Development (AMED)	Japan	Research on Regulatory Science of 427 Pharmaceuticals and Medical Devices
Japan Society for the Promotion of Science	Japan	15K06962

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2018-07-04
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary