7LFN | pdb_00007lfn

Structure of Hyperglycosylated Human IgG1 Fc (Fc267_329)

• PDB DOI: https://doi.org/10.2210/pdb7LFN/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-01-17 Released: 2021-01-27 
• Deposition Author(s): Fields, J.K., Sundberg, E.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.270 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Silent Antibodies: Generation of Hyperglycosylated FCs to Ablate Effector Functions

Fields, J.K., Sundberg, E.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 56.56 kDa 
• Atom Count: 3,315 
• Modeled Residue Count: 400 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG1 Fc (Fc267_329)	A, B	233	Homo sapiens	Mutation(s): 0  Gene Names: DKFZp686C11235
UniProt
Find proteins for Q6MZV7 (Homo sapiens) Explore Q6MZV7  Go to UniProtKB:  Q6MZV7
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

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)-[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, E	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G28663KH GlyCosmos: G28663KH GlyGen: G28663KH

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUC	F [auth A], H [auth B]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.270 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.483	α = 90
b = 79.253	β = 90
c = 141.321	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Fields, J.K., Sundberg, E.J.

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary