Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 75.60 kDa 
• Atom Count: 4768 
• Residue Count: 580 
• Unique protein chains: 2

3WJL

Crystal structure of IIb selective Fc variant, Fc(V12), in complex with FcgRIIb

• DOI: 10.2210/pdb3WJL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2013-10-11 Released: 2013-11-13 
• Deposition Author(s): Kadono, S., Mimoto, F., Katada, H., Igawa, T., Kuramochi, T., Muraoka, M., Wada, Y., Haraya, K., Miyazaki, T., Hattori, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.270 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Literature

Engineered antibody Fc variant with selectively enhanced Fc gamma RIIb binding over both Fc gamma RIIaR131 and Fc gamma RIIaH131.

Mimoto, F., Katada, H., Kadono, S., Igawa, T., Kuramochi, T., Muraoka, M., Wada, Y., Haraya, K., Miyazaki, T., Hattori, K.

(2013) Protein Eng Des Sel 26: 589-598

• PubMed: 23744091 
• DOI: 10.1093/protein/gzt022
• Primary Citation of Related Structures:  
  3WJJ, 3WJL


• PubMed Abstract: 
  

Engaging inhibitory FcγRIIb by Fc region has been recently reported to be an attractive approach for improving the efficacy of antibody therapeutics. However, the previously reported S267E/L328F variant with enhanced binding affinity to FcγRIIb, also enhances binding affinity to FcγRIIa(R131) allotype to a similar degree because FcγRIIb and FcγRIIa(R131) are structurally similar. In this study, we applied comprehensive mutagenesis and structure-guided design based on the crystal structure of the Fc/FcγRIIb complex to identify a novel Fc variant with selectively enhanced FcγRIIb binding over both FcγRIIa(R131) and FcγRIIa(H131). This novel variant has more than 200-fold stronger binding affinity to FcγRIIb than wild-type IgG1, while binding affinity to FcγRIIa(R131) and FcγRIIa(H131) is comparable with or lower than wild-type IgG1. This selectivity was achieved by conformational change of the C(H)2 domain by mutating Pro to Asp at position 238. Fc variant with increased binding to both FcγRIIb and FcγRIIa induced platelet aggregation and activation in an immune complex form in vitro while our novel variant did not. When applied to agonistic anti-CD137 IgG1 antibody, our variant greatly enhanced the agonistic activity. Thus, the selective enhancement of FcγRIIb binding achieved by our Fc variant provides a novel tool for improving the efficacy of antibody therapeutics.

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Organizational Affiliation: 

Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	A, B	230	Homo sapiens	Mutation(s): 7  Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
NIH Common Fund Data Resources
PHAROS:  P01857 GTEx:  ENSG00000211896

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Low affinity immunoglobulin gamma Fc region receptor II-c	C	179	Homo sapiens	Mutation(s): 0  Gene Names: FCGR2C, CD32, FCG2, IGFR2
Find proteins for P31995 (Homo sapiens) Explore P31995  Go to UniProtKB:  P31995
NIH Common Fund Data Resources
PHAROS:  P31995

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	8		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E	9		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.270 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.71	α = 90
b = 260.2	β = 90
c = 56.86	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-11 
• Released Date: 2013-11-13 
Deposition Author(s): Kadono, S., Mimoto, F., Katada, H., Igawa, T., Kuramochi, T., Muraoka, M., Wada, Y., Haraya, K., Miyazaki, T., Hattori, K.

Revision History 

• Version 1.0: 2013-11-13
  Type: Initial release
  
• Version 1.1: 2014-11-26
  Changes: Other
• Version 1.2: 2018-06-20
  Changes: Data collection, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary