5GSQ

Crystal structure of IgG Fc with a homogeneous glycoform and Antibody-Dependent Cellular Cytotoxicity

• PDB DOI: https://doi.org/10.2210/pdb5GSQ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2016-08-17 Released: 2017-06-28 
• Deposition Author(s): Chen, C.-L., Hsu, J.-C., Lin, C.-W., Wu, C.-Y., Wong, C.-H., Ma, C.
• Funding Organization(s): Academia Sinica

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.267 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 106.42 kDa 
• Atom Count: 7,717 
• Modelled Residue Count: 818 
• Deposited Residue Count: 900 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	A, B, C, D	225	Homo sapiens	Mutation(s): 0  Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896

Oligosaccharides

Help

Entity ID: 2
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)-[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	E, F	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G28663KH GlyCosmos:  G28663KH GlyGen:  G28663KH

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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	G	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G88421PE GlyCosmos:  G88421PE GlyGen:  G88421PE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G00432WW GlyCosmos:  G00432WW

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.267 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.183	α = 90
b = 158.406	β = 109.04
c = 66.905	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Chen, C.-L., Hsu, J.-C., Lin, C.-W., Wu, C.-Y., Wong, C.-H., Ma, C.

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Funding Organization	Location	Grant Number
Academia Sinica	Taiwan	--

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Data collection
• Version 2.0: 2020-03-18
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary