9GW5 | pdb_00009gw5

type-I interferon autoantibodies pmab3, pmab19 and pmab14 in complex with Interferon alpha-2

PDB DOI: https://doi.org/10.2210/pdb9GW5/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2024-09-26 Released: 2025-10-08
Deposition Author(s): Duquerroy, S., Rey, F., Mahevas, M., Chappert, P., Ahouzi, O.
Funding Organization(s): French National Research Agency, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Fondation pour la Recherche Medicale (FRM)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free:
0.324 (Depositor), 0.302 (DCC)
R-Value Work:
0.294 (Depositor)
R-Value Observed:
0.296 (Depositor)

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Temporal and structural insights into type-I interferons autoantibodies in severe COVID-19

Vanderkerken, M., Fournier, M., Dorgham, K., Bastard, P., Ahouzi, O., Duquerroy, S., Nguyen, N.K., Broutin, M., Charlet, M., Vandenberghe, A., Bizien, L., Da Mata-Jardin, O., Haouz, A., Belmondo, T., Hue, S., Borghesi, A., Rodriguez-Gallego, C., Vinh, D., Andreakos, V., Haerynck, F., Halwani, R., Hammerstrom, T.Q.P., Bjorkstrom, N., Strunz, B., Mogensen, T., Trouillet, S., Neven, B., Levy, R., Le Voyer, T., Delmonte, O., O'Farrelly, C., Riviere, J., Amador Borrero, B., Servettaz, A., Crickx, E., Michel, M., Puel, A., Abel, L., Luyt, C.E., Mathian, A., Amoura, Z., weill, J.C., Casanova, J.L., Rey, F.A., Gorochov, G., Chappert, P., Mahevas, M.

To be published.

Macromolecule Content

Total Structure Weight: 111.84 kDa
Atom Count: 6,368
Modeled Residue Count: 830
Deposited Residue Count: 1,051
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon alpha-2	A	188	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01563
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
type-I interferons autoantibody pamb14 heavy chain	B [auth H]	290	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv type-I interferons autoantibody pamb03	C [auth U]	288	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv type-I interferons autoantibody pamb19	D [auth V]	285	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.324 (Depositor), 0.302 (DCC)
R-Value Work: 0.294 (Depositor)
R-Value Observed: 0.296 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.216	α = 90
b = 166.216	β = 90
c = 190.135	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
autoPROC	data processing
STARANISO	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-22-CE15-0047-01
French National Research Agency	France	ANR-24-CHBS-0003
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI088364
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI163029
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21AI160576
French National Research Agency	France	ANR-10-IAHU-01
French National Research Agency	France	ANR-10-LABX-62-IBEID
Fondation pour la Recherche Medicale (FRM)	France	EQU201903007798
French National Research Agency	France	ANR-20-CE93-003
French National Research Agency	France	ANR-21-LIBA-0002
French National Research Agency	France	ANR-21-RHUS-08