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- PDB-10fj: FcgRIIa in complex with IV.3 Fab -

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Basic information

Entry
Database: PDB / ID: 10fj
TitleFcgRIIa in complex with IV.3 Fab
Components
  • IV.3 Fab heavy chain
  • IV.3 Fab light chain
  • Low affinity immunoglobulin gamma Fc region receptor II-a
KeywordsIMMUNE SYSTEM / platelet / FcgRIIa / mAb IV.3
Function / homology
Function and homology information


IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / positive regulation of phagocytosis / FCGR3A-mediated IL10 synthesis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production ...IgG receptor activity / antibody-dependent cellular cytotoxicity / IgG binding / FCGR activation / Role of phospholipids in phagocytosis / positive regulation of phagocytosis / FCGR3A-mediated IL10 synthesis / secretory granule membrane / Regulation of actin dynamics for phagocytic cup formation / positive regulation of tumor necrosis factor production / cell surface receptor signaling pathway / external side of plasma membrane / Neutrophil degranulation / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Low affinity immunoglobulin gamma Fc region receptor II-a
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsColler, B.S. / Wang, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5R01HL019278-48 United States
CitationJournal: bioRxiv / Year: 2026
Title: Mechanistic Basis for the Selective Recognition of the Fcγ Receptor IIa by Monoclonal Antibody IV.3.
Authors: Jialing Wang / Sabina Novack / Jihong Li / Emily G Niejadlik / Stylianos Bournazos / Barry S Coller / Marta Filizola
Abstract: The monoclonal antibody IV.3 selectively binds the platelet Fcγ receptor IIa (FcγRIIa), potently blocking immune complex engagement without cross-reacting with the closely-related FcγRIIb. This ...The monoclonal antibody IV.3 selectively binds the platelet Fcγ receptor IIa (FcγRIIa), potently blocking immune complex engagement without cross-reacting with the closely-related FcγRIIb. This specificity has made IV.3 invaluable for dissecting FcγRIIa-mediated activation in diverse conditions, including infection, autoimmunity, thromboinflammation, and platelet-mediated thrombosis. We combined cryogenic electron microscopy, surface plasmon resonance, alchemical free energy calculations, and molecular dynamics simulations to elucidate IV.3's binding sites on FcγRIIa and the mechanistic basis of IV.3 specificity. We find that IV.3 engages a broader FcγRIIa epitope than previously recognized, extending beyond residues H/R134 and L135 (R and S in FcγRIIb). Simulations of FcγIIa-R134 variants bearing either L135 or S135 reveal that IV.3 specificity arises from hydrophobic stabilization mediated by L135 and disruption of an R134-specific interaction network in the presence of S135. These findings provide a mechanistic framework for rational design of FcγRIIa-targeted therapeutics.
History
DepositionJan 16, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low affinity immunoglobulin gamma Fc region receptor II-a
H: IV.3 Fab heavy chain
L: IV.3 Fab light chain


Theoretical massNumber of molelcules
Total (without water)71,9513
Polymers71,9513
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Low affinity immunoglobulin gamma Fc region receptor II-a / IgG Fc receptor II-a / CDw32 / Fc-gamma RII-a / Fc-gamma-RIIa / FcRII-a


Mass: 20528.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR2A, CD32, FCG2, FCGR2A1, IGFR2 / Production host: Homo sapiens (human) / References: UniProt: P12318
#2: Antibody IV.3 Fab heavy chain


Mass: 25493.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody IV.3 Fab light chain


Mass: 25928.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1fcgRIIa-IV.3 Fab complexCOMPLEXall0MULTIPLE SOURCES
2fcgRIIaCOMPLEX#11RECOMBINANT
3IV.3 FabCOMPLEX#2-#31RECOMBINANT
Molecular weightValue: 0.75 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCV4.4.0particle selection
13cryoSPARCV4.4.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 392060 / Symmetry type: POINT

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