6WNA | pdb_00006wna

Next generation monomeric IgG4 Fc

• PDB DOI: https://doi.org/10.2210/pdb6WNA/pdb

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


• Deposited: 2020-04-22 Released: 2021-09-15 
• Deposition Author(s): Oganesyan, V.Y., Shan, L., van Dyk, N., Dall'Acqua, W.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.263 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Models: experimental

Literature

In vivo pharmacokinetic enhancement of monomeric Fc and monovalent bispecific designs through structural guidance.

Shan, L., Dyk, N.V., Haskins, N., Cook, K.M., Rosenthal, K.L., Mazor, R., Dragulin-Otto, S., Jiang, Y., Wu, H., Dall'Acqua, W.F., Borrok, M.J., Damschroder, M.M., Oganesyan, V.

(2021) Commun Biol 4: 1048-1048

• PubMed: 34497355 
• DOI: https://doi.org/10.1038/s42003-021-02565-5
• Primary Citation Related Structures: 
  6WIB, 6WMH, 6WNA, 6WOL


• PubMed Abstract: 
  

  In a biologic therapeutic landscape that requires versatility in targeting specificity, valency and half-life modulation, the monomeric Fc fusion platform holds exciting potential for the creation of a class of monovalent protein therapeutics that includes fusion proteins and bispecific targeting molecules. Here we report a structure-guided approach to engineer monomeric Fc molecules to adapt multiple versions of half-life extension modifications. Co-crystal structures of these monomeric Fc variants with Fc neonatal receptor (FcRn) shed light into the binding interactions that could serve as a guide for engineering the half-life of antibody Fc fragments. These engineered monomeric Fc molecules also enabled the generation of a novel monovalent bispecific molecular design, which translated the FcRn binding enhancement to improvement of in vivo serum half-life.

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Organizational Affiliation: 
• Antibody Discovery and Protein Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA. [e-mail].
Denali Therapeutics, South San Francisco, CA, USA. [e-mail].
Antibody Discovery and Protein Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA.
Early Oncology, R&D, AstraZeneca, Gaithersburg, MD, USA.
Division of Cellular and Gene Therapies, FDA Center for Biologics Evaluation and Research, Silver Spring, MD, USA.
Dosage Form Design and Development, R&D, AstraZeneca, Gaithersburg, MD, USA.
Clinical Pharmacology and Safety Science, R&D, AstraZeneca, Gaithersburg, MD, USA.
Janssen BioTherapeutics, Janssen Research and Development, Spring House, PA, USA.
Antibody Discovery and Protein Engineering, R&D, AstraZeneca, Gaithersburg, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 66.6 kDa 
• Atom Count: 4,728 
• Modeled Residue Count: 563 
• Deposited Residue Count: 570 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG receptor FcRn large subunit p51	A	264	Homo sapiens	Mutation(s): 0  Gene Names: FCGRT, FCRN
UniProt & NIH Common Fund Data Resources
Find proteins for P55899 (Homo sapiens) Explore P55899  Go to UniProtKB:  P55899
PHAROS:  P55899 GTEx:  ENSG00000104870

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin heavy constant gamma 4	C [auth H]	207	Homo sapiens	Mutation(s): 9  Gene Names: IGHG4
UniProt & NIH Common Fund Data Resources
Find proteins for P01861 (Homo sapiens) Explore P01861  Go to UniProtKB:  P01861
PHAROS:  P01861 GTEx:  ENSG00000211892
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P01861-2

Oligosaccharides

Help  

Entity ID: 4
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)-[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 [auth C]	9		N-Glycosylation
Glycosylation Resources
GlyTouCan: G27919IH GlyCosmos: G27919IH GlyGen: G27919IH

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.263 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.095	α = 90
b = 122.096	β = 90
c = 179.446	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Oganesyan, V.Y., Shan, L., van Dyk, N., Dall'Acqua, W.F.

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2021-09-22
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary