4YPG

Structural Insights Into the Neutralization Properties of a Human Anti-Interferon Monoclonal Antibody

• PDB DOI: https://doi.org/10.2210/pdb4YPG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-12 Released: 2015-05-06 
• Deposition Author(s): Oganesyan, V., Dall'Acqua, W.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.272 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

Structural Insights into the Neutralization Properties of the Fully Human, Anti-interferon Monoclonal Antibody Sifalimumab.

Oganesyan, V., Peng, L., Woods, R.M., Wu, H., Dall'Acqua, W.F.

(2015) J Biol Chem 290: 14979-14985

• PubMed: 25925951 
• DOI: https://doi.org/10.1074/jbc.M115.652156
• Primary Citation of Related Structures:  
  4YPG


• PubMed Abstract: 
  

  We report the three-dimensional structure of human interferon α-2A (IFN-α2A) bound to the Fab fragment of a therapeutic monoclonal antibody (sifalimumab; IgG1/κ). The structure of the corresponding complex was solved at a resolution of 3.0 Å using molecular replacement and constitutes the first reported structure of a human type I IFN bound to a therapeutic antibody. This study revealed the major contribution made by the first complementarity-determining region in each of sifalimumab light and heavy chains. These data also provided the molecular basis for sifalimumab mechanism of action. We propose that its interferon-neutralizing properties are the result of direct competition for IFN-α2A binding to the IFN receptor subunit 1 (IFNAR1) and do not involve inhibiting IFN-α2A binding to the IFN receptor subunit 2 (IFNAR2).

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Organizational Affiliation: 

From the Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, Maryland 20878 [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 131.15 kDa 
• Atom Count: 9,219 
• Modelled Residue Count: 1,188 
• Deposited Residue Count: 1,190 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sifalimumab light chain	A, F [auth L]	215	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q6PJF2 (Homo sapiens) Explore Q6PJF2  Go to UniProtKB:  Q6PJF2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sifalimumab heavy chain	B, E [auth H]	219	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon alpha-2	C, D	161	Homo sapiens	Mutation(s): 0  Gene Names: IFNA2, IFNA2A, IFNA2B, IFNA2C
UniProt & NIH Common Fund Data Resources
Find proteins for P01563 (Homo sapiens) Explore P01563  Go to UniProtKB:  P01563
GTEx:  ENSG00000188379

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	G [auth A], H [auth B], I [auth C], J [auth D], K [auth H], L	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.272 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.82	α = 90
b = 153.26	β = 90
c = 163.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Oganesyan, V., Dall'Acqua, W.F.

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2015-05-13
  Changes: Database references
• Version 1.2: 2015-06-24
  Changes: Database references
• Version 2.0: 2019-02-13
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description