5YC5

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 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

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 
• Modelled 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

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	3D 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	3D 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 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• 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