3SGJ

Unique carbohydrate-carbohydrate interactions are required for high affinity binding between FcgIII and antibodies lacking core fucose

• PDB DOI: https://doi.org/10.2210/pdb3SGJ/pdb

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


• Deposited: 2011-06-15 Released: 2011-08-03 
• Deposition Author(s): Ferrara, C., Grau, S., Jaeger, C., Sondermann, P., Bruenker, P., Waldhauer, I., Hennig, M., Ruf, A., Rufer, A.C., Stihle, M., Umana, P., Benz, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.252 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

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 and generated by PISA (software)

Biological Assembly 2  

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 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.42 kDa 
• Atom Count: 5,443 
• Modelled Residue Count: 605 
• Deposited Residue Count: 654 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
human Fc fragment	A, B	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
human Fcg3a receptor	C	204	Homo sapiens	Mutation(s): 3  Gene Names: CD16A, FCG3, FCGR3, FCGR3A, 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
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	D, E	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80858MF GlyCosmos:  G80858MF GlyGen:  G80858MF

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(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	F	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	H [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.252 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.654	α = 90
b = 88.478	β = 90
c = 140.29	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Ferrara, C., Grau, S., Jaeger, C., Sondermann, P., Bruenker, P., Waldhauer, I., Hennig, M., Ruf, A., Rufer, A.C., Stihle, M., Umana, P., Benz, J.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary