4J12 | pdb_00004j12

monomeric Fc

• PDB DOI: https://doi.org/10.2210/pdb4J12/pdb

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


• Deposited: 2013-01-31 Released: 2013-05-01 
• Deposition Author(s): Ishino, T., Wang, M., Mosyak, L., Tam, A., Duan, W., Svenson, K., Joyce, A., O'Hara, D., Lin, L., Somers, W., Kriz, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.238 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Engineering a Monomeric Fc Domain Modality by N-Glycosylation for the Half-life Extension of Biotherapeutics.

Ishino, T., Wang, M., Mosyak, L., Tam, A., Duan, W., Svenson, K., Joyce, A., O'Hara, D.M., Lin, L., Somers, W.S., Kriz, R.

(2013) J Biological Chem 288: 16529-16537

• PubMed: 23615911 
• DOI: https://doi.org/10.1074/jbc.M113.457689
• Primary Citation Related Structures: 
  4J12


• PubMed Abstract: 
  

  Human IgG is a bivalent molecule that has two identical Fab domains connected by a dimeric Fc domain. For therapeutic purposes, however, the bivalency of IgG and Fc fusion proteins could cause undesired properties. We therefore engineered the conversion of the natural dimeric Fc domain to a highly soluble monomer by introducing two Asn-linked glycans onto the hydrophobic C(H)3-C(H)3 dimer interface. The monomeric Fc (monoFc) maintained the binding affinity for neonatal Fc receptor (FcRn) in a pH-dependent manner. We solved the crystal structure of monoFc, which explains how the carbohydrates can stabilize the protein surface and provides the rationale for molecular recognition between monoFc and FcRn. The monoFc prolonged the in vivo half-life of an antibody Fab domain, and a tandem repeat of the monoFc further prolonged the half-life. This monoFc modality can be used to improve the pharmacokinetics of monomeric therapeutic proteins with an option to modulate the degree of half-life extension.

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Organizational Affiliation: 
• From Global Biotherapeutics Technologies, Pfizer Inc., Cambridge, Massachusetts 02140. Electronic address: [e-mail].
Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Andover, Massachusetts 01810.
From Global Biotherapeutics Technologies, Pfizer Inc., Cambridge, Massachusetts 02140.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.33 kDa 
• Atom Count: 1,927 
• Modeled Residue Count: 209 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
human Fc fragment	A	210	Homo sapiens	Mutation(s): 3
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P01857-2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G39213VZ GlyCosmos: G39213VZ GlyGen: G39213VZ

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.238 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.224	α = 90
b = 64.224	β = 90
c = 146.937	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Ishino, T., Wang, M., Mosyak, L., Tam, A., Duan, W., Svenson, K., Joyce, A., O'Hara, D., Lin, L., Somers, W., Kriz, R.

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2013-07-24
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2018-06-13
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-11-27
  Changes: Data collection, Database references, Structure summary