9GVO | pdb_00009gvo

type-I interferons autoantibodies pmab15 and pmab14 in complex with Interferon alpha-2

PDB DOI: https://doi.org/10.2210/pdb9GVO/pdb

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

Deposited: 2024-09-25 Released: 2025-10-08
Deposition Author(s): Duquerroy, S., Rey, F., Ahouzi, O., Mahevas, M., Chappert, P.
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: 1.81 Å
R-Value Free:
0.215 (Depositor), 0.206 (DCC)
R-Value Work:
0.193 (Depositor), 0.182 (DCC)
R-Value Observed:
0.194 (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., Rodriguez-Gallego, C., 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: 83.35 kDa
Atom Count: 5,172
Modeled Residue Count: 606
Deposited Residue Count: 772
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv type-I interferons autoantibody pmab14	A	290	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon alpha-2	B	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01563
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv type-I interferons autoantibody pmab15	C [auth H]	294	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain L [auth H] SDF format, chain I [auth B] MOL2 format, chain L [auth H] MOL2 format, chain I [auth B] mmCIF format, chain L [auth H] mmCIF format, chain I [auth B]	I [auth B], L [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth B] Focus chain L [auth H] Interactions & Density Focus chain I [auth B] Focus chain L [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth H] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth H] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth H] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A] E [auth B] F [auth B] G [auth B] H [auth B] D [auth A], E [auth B], F [auth B], G [auth B], H [auth B], K [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth H] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth H]
K Query on K Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.215 (Depositor), 0.206 (DCC)
R-Value Work: 0.193 (Depositor), 0.182 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.93	α = 90
b = 112.93	β = 90
c = 155.974	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

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