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- PDB-9r2e: Structure of ARGX-121 Fab fragment in complex with the Fc fragmen... -

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Basic information

Entry
Database: PDB / ID: 9r2e
TitleStructure of ARGX-121 Fab fragment in complex with the Fc fragment of IgA1
Components
  • (ARGX-121 Fab fragment ...) x 2
  • Isoform 1 of Immunoglobulin heavy constant alpha 1
KeywordsIMMUNE SYSTEM / Antibody / IgA mediated autoimmunity / immunoglobulin / PROTEROS BIOSTRUCTURES GMBH
Function / homology
Function and homology information


secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA immunoglobulin complex / glomerular filtration / IgG immunoglobulin complex / immunoglobulin complex, circulating / positive regulation of respiratory burst / complement activation, classical pathway / Scavenging of heme from plasma ...secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA immunoglobulin complex / glomerular filtration / IgG immunoglobulin complex / immunoglobulin complex, circulating / positive regulation of respiratory burst / complement activation, classical pathway / Scavenging of heme from plasma / antigen binding / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / antibacterial humoral response / blood microparticle / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Immunoglobulin heavy constant alpha 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsPannecoucke, E. / Voet, S. / Deweirdt, L. / Verbeiren, J. / Gabriels, S. / Provost, M. / Freier, R. / Koenig, J. / Lammens, A. / Silence, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of ARGX-121 Fab fragment in complex with the Fc fragment of IgA1
Authors: Voet, S. / Provost, M. / Deweirdt, L. / Verbeiren, J. / Gabriels, S. / Silence, K. / Pannecoucke, E.
History
DepositionApr 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: ARGX-121 Fab fragment heavy chain
L: ARGX-121 Fab fragment light chain
P: Isoform 1 of Immunoglobulin heavy constant alpha 1
Q: Isoform 1 of Immunoglobulin heavy constant alpha 1
A: ARGX-121 Fab fragment heavy chain
B: ARGX-121 Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,42218
Polymers147,5706
Non-polymers85212
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15390 Å2
ΔGint-68 kcal/mol
Surface area57620 Å2
Unit cell
Length a, b, c (Å)77.291, 232.312, 105.519
Angle α, β, γ (deg.)90, 90.35, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11P-501-

MG

21B-301-

MG

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Components

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Protein , 1 types, 2 molecules PQ

#3: Protein Isoform 1 of Immunoglobulin heavy constant alpha 1 / Ig alpha-1 chain C region / Ig alpha-1 chain C region BUR / Ig alpha-1 chain C region TRO


Mass: 23155.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHA1 / Production host: Homo sapiens (human) / References: UniProt: P01876

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Antibody , 2 types, 4 molecules HALB

#1: Antibody ARGX-121 Fab fragment heavy chain


Mass: 25904.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody ARGX-121 Fab fragment light chain


Mass: 24725.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 4 types, 389 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 16% (w/v) PEG8000, 20% (v/v) Glycerol, 0.16 M MgAcetate, 0.08 M Na Cacodylate pH 6.50

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jan 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 2.539→116.16 Å / Num. obs: 59436 / % possible obs: 97.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 4.1
Reflection shellResolution: 2.539→2.583 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.592 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3039 / Rsym value: 1.592 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
XDSJun 30, 2023data reduction
autoPROC1.1.7data scaling
Aimless0.7.13data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→116.16 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25182 2937 -RANDOM
Rwork0.21095 ---
obs0.21306 55813 96.1 %-
Displacement parametersBiso mean: 53.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å2-0.13 Å2
2---0.9 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.54→116.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9611 0 54 377 10042
LS refinement shellResolution: 2.54→2.583 Å /
Rfactor% reflection
Rfree0.338 -
Rwork0.328 -
obs-89.26 %

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