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- PDB-8y31: The crystal structure of the QX006N-Fab/IFNAR1-SD123 complex -

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Basic information

Entry
Database: PDB / ID: 8y31
TitleThe crystal structure of the QX006N-Fab/IFNAR1-SD123 complex
Components
  • Interferon alpha/beta receptor 1
  • QX006N-Fab-HC
  • QX006N-Fab-LC
KeywordsIMMUNE SYSTEM / IFNAR1 / QX006N / the QX006N-Fab-IFNAR1-SD123 complex
Function / homology
Function and homology information


type I interferon receptor activity / type I interferon binding / JAK pathway signal transduction adaptor activity / cellular response to interferon-alpha / positive regulation of cellular respiration / type I interferon-mediated signaling pathway / cytokine binding / Regulation of IFNA/IFNB signaling / cell surface receptor signaling pathway via JAK-STAT / cellular response to interferon-beta ...type I interferon receptor activity / type I interferon binding / JAK pathway signal transduction adaptor activity / cellular response to interferon-alpha / positive regulation of cellular respiration / type I interferon-mediated signaling pathway / cytokine binding / Regulation of IFNA/IFNB signaling / cell surface receptor signaling pathway via JAK-STAT / cellular response to interferon-beta / Evasion by RSV of host interferon responses / response to virus / cellular response to virus / Interferon alpha/beta signaling / late endosome / response to lipopolysaccharide / Potential therapeutics for SARS / lysosome / receptor complex / SARS-CoV-2 activates/modulates innate and adaptive immune responses / plasma membrane
Similarity search - Function
Interferon alpha/beta receptor 1 / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interferon alpha/beta receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsLi, W. / Feng, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071191 China
National Natural Science Foundation of China (NSFC)31971160 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural basis for the recognition of IFNAR1 by the humanized therapeutic monoclonal antibody QX006N for the treatment of systemic lupus erythematosus.
Authors: Chen, X. / Ke, H. / Li, W. / Yin, L. / Chen, W. / Chen, T. / Wu, Y. / Qiu, J. / Feng, W.
History
DepositionJan 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: QX006N-Fab-LC
B: QX006N-Fab-HC
C: QX006N-Fab-LC
D: QX006N-Fab-HC
E: Interferon alpha/beta receptor 1
F: Interferon alpha/beta receptor 1


Theoretical massNumber of molelcules
Total (without water)174,9716
Polymers174,9716
Non-polymers00
Water1,22568
1
A: QX006N-Fab-LC
B: QX006N-Fab-HC
E: Interferon alpha/beta receptor 1


Theoretical massNumber of molelcules
Total (without water)87,4853
Polymers87,4853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: QX006N-Fab-LC
D: QX006N-Fab-HC
F: Interferon alpha/beta receptor 1


Theoretical massNumber of molelcules
Total (without water)87,4853
Polymers87,4853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.155, 121.031, 79.738
Angle α, β, γ (deg.)90.00, 111.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody QX006N-Fab-LC


Mass: 23200.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody QX006N-Fab-HC


Mass: 24517.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Interferon alpha/beta receptor 1 / IFN-R-1 / IFN-alpha/beta receptor 1 / Cytokine receptor class-II member 1 / Cytokine receptor ...IFN-R-1 / IFN-alpha/beta receptor 1 / Cytokine receptor class-II member 1 / Cytokine receptor family 2 member 1 / CRF2-1 / Type I interferon receptor 1


Mass: 39767.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR1, IFNAR / Production host: Homo sapiens (human) / References: UniProt: P17181
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.41 %
Crystal growTemperature: 289 K / Method: evaporation, recrystallization
Details: 8%(w/v) PEG3350 50 mM Na-Citrate pH 5.5, 100 mM (NH4)2Citrate, 250 mM NaCl, 5 mM Hexadecyltrimethylammonium Bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.68→68.06 Å / Num. obs: 35675 / % possible obs: 98.6 % / Redundancy: 5.6 % / CC1/2: 0.993 / Net I/σ(I): 12.8
Reflection shellResolution: 2.68→2.83 Å / Num. unique obs: 3527 / CC1/2: 0.672

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→46.89 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 1747 4.9 %
Rwork0.1944 --
obs0.1965 35675 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8262 0 0 68 8330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048452
X-RAY DIFFRACTIONf_angle_d0.77511496
X-RAY DIFFRACTIONf_dihedral_angle_d20.2093022
X-RAY DIFFRACTIONf_chiral_restr0.0491288
X-RAY DIFFRACTIONf_plane_restr0.0051470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.760.37641490.28162784X-RAY DIFFRACTION98
2.76-2.850.28061600.24462799X-RAY DIFFRACTION99
2.85-2.950.31021530.23842822X-RAY DIFFRACTION99
2.95-3.070.26131690.2292812X-RAY DIFFRACTION99
3.07-3.210.29561510.21422813X-RAY DIFFRACTION99
3.21-3.380.26141130.21252856X-RAY DIFFRACTION99
3.38-3.590.26471510.21672779X-RAY DIFFRACTION98
3.59-3.870.25991310.20132827X-RAY DIFFRACTION99
3.87-4.260.21921500.18242824X-RAY DIFFRACTION98
4.26-4.880.22391300.1562860X-RAY DIFFRACTION99
4.88-6.140.20021680.17552843X-RAY DIFFRACTION99
6.14-46.890.17381220.17322909X-RAY DIFFRACTION99

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