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- PDB-9gw5: type-I interferon autoantibodies pmab3, pmab19 and pmab14 in comp... -

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Basic information

Entry
Database: PDB / ID: 9gw5
Titletype-I interferon autoantibodies pmab3, pmab19 and pmab14 in complex with Interferon alpha-2
Components
  • Interferon alpha-2
  • scFv type-I interferons autoantibody pamb03
  • scFv type-I interferons autoantibody pamb19
  • type-I interferons autoantibody pamb14 heavy chain
KeywordsIMMUNE SYSTEM / type-I interferon / Interferon alpha-2 / autoantibody / antigen antibody complex / COVID-19 pneumonia / Signaling Protein
Function / homology
Function and homology information


type I interferon receptor binding / B cell activation involved in immune response / natural killer cell activation involved in immune response / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / host-mediated suppression of symbiont invasion / cell surface receptor signaling pathway via STAT ...type I interferon receptor binding / B cell activation involved in immune response / natural killer cell activation involved in immune response / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / host-mediated suppression of symbiont invasion / cell surface receptor signaling pathway via STAT / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / response to exogenous dsRNA / humoral immune response / Regulation of IFNA/IFNB signaling / cytokine activity / Evasion by RSV of host interferon responses / cellular response to virus / Interferon alpha/beta signaling / cell-cell signaling / : / Factors involved in megakaryocyte development and platelet production / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region
Similarity search - Function
Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsDuquerroy, S. / Rey, F. / Mahevas, M. / Chappert, P. / Ahouzi, O.
Funding support France, United States, 11items
OrganizationGrant numberCountry
French National Research AgencyANR-22-CE15-0047-01 France
French National Research AgencyANR-24-CHBS-0003 France
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI088364 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI163029 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI160576 United States
French National Research AgencyANR-10-IAHU-01 France
French National Research AgencyANR-10-LABX-62-IBEID France
Fondation pour la Recherche Medicale (FRM)EQU201903007798 France
French National Research AgencyANR-20-CE93-003 France
French National Research AgencyANR-21-LIBA-0002 France
French National Research AgencyANR-21-RHUS-08 France
CitationJournal: To Be Published
Title: Temporal and structural insights into type-I interferons autoantibodies in severe COVID-19
Authors: 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. / ...Authors: 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.
History
DepositionSep 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon alpha-2
H: type-I interferons autoantibody pamb14 heavy chain
U: scFv type-I interferons autoantibody pamb03
V: scFv type-I interferons autoantibody pamb19


Theoretical massNumber of molelcules
Total (without water)111,8394
Polymers111,8394
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, antigen antibody complexes
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.216, 166.216, 190.135
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Interferon alpha-2 / IFN-alpha-2 / Interferon alpha-A / LeIF A


Mass: 21581.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNA2, IFNA2A, IFNA2B, IFNA2C / Cell line (production host): Schneider S2 Cell / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01563
#2: Antibody type-I interferons autoantibody pamb14 heavy chain


Mass: 30179.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Single chain fragment variable (scFv) polypeptide chain with heavy and light components part of the same chain.
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Schneider S2 Cell / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody scFv type-I interferons autoantibody pamb03


Mass: 30131.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Schneider S2 Cell / Production host: Drosophila melanogaster (fruit fly)
#4: Antibody scFv type-I interferons autoantibody pamb19


Mass: 29945.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Schneider S2 Cell / Production host: Drosophila melanogaster (fruit fly)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes pH 7.5 1.9 (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.953721 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953721 Å / Relative weight: 1
ReflectionResolution: 4→150 Å / Num. obs: 13477 / % possible obs: 98.7 % / Redundancy: 79 % / CC1/2: 0.996 / Rmerge(I) obs: 0.781 / Rpim(I) all: 0.128 / Rrim(I) all: 0.786 / Net I/σ(I): 8.8
Reflection shellResolution: 4→4.128 Å / Redundancy: 81.5 % / Rmerge(I) obs: 8.869 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1038 / CC1/2: 0.686 / Rpim(I) all: 1.379 / Rrim(I) all: 8.923 / % possible all: 86.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→25 Å / Cor.coef. Fo:Fc: 0.852 / Cor.coef. Fo:Fc free: 0.836 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.899
RfactorNum. reflection% reflectionSelection details
Rfree0.3236 645 -RANDOM
Rwork0.2943 ---
obs0.2958 13185 97.2 %-
Displacement parametersBiso mean: 151.33 Å2
Baniso -1Baniso -2Baniso -3
1--2.8566 Å20 Å20 Å2
2---2.8566 Å20 Å2
3---5.7131 Å2
Refine analyzeLuzzati coordinate error obs: 0.67 Å
Refinement stepCycle: LAST / Resolution: 4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6368 0 0 0 6368
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0066510HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.848824HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2196SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1094HARMONIC5
X-RAY DIFFRACTIONt_it6510HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion855SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4200SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion16.57
LS refinement shellResolution: 4→4.07 Å
RfactorNum. reflection% reflection
Rfree0.3061 17 -
Rwork0.2956 --
obs0.296 413 65.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.799-1.30411.72916.64841.58538.3155-0.16950.3085-0.18580.30850.1026-0.0327-0.1858-0.03270.06690.0581-0.20530.1369-0.05590.06690.1709-46.3586-30.12511.4826
22.8152-2.046-0.55396.51370.66771.87350.08430.12420.35530.1242-0.19620.17360.35530.17360.112-0.10610.03880.01-0.1220.1554-0.304-19.0034-22.03012.3227
38.31240.0018-1.58328.3185-3.07878.3155-0.15320.30860.68640.30860.119-0.20220.6864-0.20220.03420.4301-0.07280.14680.17790.04970.304-65.6734-41.150926.2603
42.54090.54642.90318.63140.79258.1014-0.1920.3864-0.63570.38640.07830.0125-0.63570.01250.11370.2690.10090.1922-0.1985-0.06450.1969-57.7954-1.66563.4931
55.51680.59710.96714.2275-0.63058.3155-0.0356-0.2114-0.2844-0.2114-0.0114-0.2202-0.2844-0.22020.047-0.15840.14720.0062-0.1825-0.07010.0835-58.3663-12.4688-15.3776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|9 - A|157 }A9 - 157
2X-RAY DIFFRACTION2{ U|3 - U|251 }U3 - 251
3X-RAY DIFFRACTION3{ V|3 - V|244 }V3 - 244
4X-RAY DIFFRACTION4{ H|4 - H|122 }H4 - 122
5X-RAY DIFFRACTION5{ H|433 - H|542 }H433 - 542

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