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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.272 (Depositor), 0.280 (DCC)
R-Value Work:
0.206 (Depositor), 0.230 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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).

Organizational Affiliation

From the Department of Antibody Discovery and Protein Engineering, MedImmune LLC, Gaithersburg, Maryland 20878 oganesyanv@medimmune.com.

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

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6PJF2
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sifalimumab heavy chain	B, E [auth H]	219	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
PHAROS: P01563 GTEx: ENSG00000188379
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01563
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain L SDF format, chain J [auth D] SDF format, chain K [auth H] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L MOL2 format, chain J [auth D] MOL2 format, chain K [auth H] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain L mmCIF format, chain J [auth D] mmCIF format, chain K [auth H]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth H] G [auth A], H [auth B], I [auth C], J [auth D], K [auth H], L	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth H] Focus chain L Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth H] Focus chain L

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.272 (Depositor), 0.280 (DCC)
R-Value Work: 0.206 (Depositor), 0.230 (DCC)
R-Value Observed: 0.209 (Depositor)

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-05-06

Deposition Author(s):

Oganesyan, V.

Dall'Acqua, W.F.

Revision History (Full details and data files)

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
Version 2.2: 2024-10-23
Changes: Structure summary