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- PDB-9td2: Integrin AlphaIIbBeta3 bound to Fab of the anti-HPA-1a antibody 26.4 -

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Basic information

Entry
Database: PDB / ID: 9td2
TitleIntegrin AlphaIIbBeta3 bound to Fab of the anti-HPA-1a antibody 26.4
Components
  • (Antibody 26.4 Fab ...) x 2
  • Integrin alpha-IIb
  • Integrin beta-3
KeywordsCELL ADHESION / Human Platelet Antigen / FNAIT / alloantibody / cryo-EM
Function / homology
Function and homology information


regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / response to platelet-derived growth factor / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / platelet alpha granule membrane ...regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / response to platelet-derived growth factor / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / positive regulation of glomerular mesangial cell proliferation / smooth muscle cell migration / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / positive regulation of leukocyte migration / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor signaling pathway / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / positive regulation of bone resorption / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / cell-cell adhesion mediated by integrin / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of cell adhesion mediated by integrin / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / negative regulation of low-density lipoprotein particle clearance / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of smooth muscle cell migration / integrin complex / glycinergic synapse / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / cell adhesion mediated by integrin / positive regulation of osteoblast proliferation / negative chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / cellular response to insulin-like growth factor stimulus / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / protein disulfide isomerase activity / microvillus membrane / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of endothelial cell apoptotic process / TGF-beta receptor signaling activates SMADs / Fibrin formation / fibronectin binding / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / Integrin cell surface interactions / ECM proteoglycans / substrate adhesion-dependent cell spreading / positive regulation of T cell migration / cell-matrix adhesion / embryo implantation / coreceptor activity / Integrin signaling / positive regulation of endothelial cell proliferation / cell adhesion molecule binding / positive regulation of endothelial cell migration / positive regulation of smooth muscle cell proliferation / integrin-mediated signaling pathway / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / response to activity / regulation of actin cytoskeleton organization / protein kinase C binding / wound healing / Signal transduction by L1 / cellular response to xenobiotic stimulus / virus receptor activity / cell-cell adhesion / platelet activation / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / VEGFA-VEGFR2 Pathway / platelet aggregation / integrin binding / blood coagulation / cellular response to mechanical stimulus / ruffle membrane / positive regulation of angiogenesis / angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / : / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin alpha Ig-like domain 3 / Integrin_b_cyt / : / Integrin EGF domain ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / : / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin alpha Ig-like domain 3 / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / EGF-like domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin alpha cytoplasmic region / : / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / EGF-like domain signature 1. / EGF-like domain signature 2. / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
Authorsde Pereda, J.M. / Stam, W. / Gragera, M. / van der Meer, F. / Chichon, F.J. / Zarkadas, E. / van der Schoot, E. / Vidarsson, G. / Takagi, J. / Margadant, C.
Funding support Netherlands, Spain, European Union, 6items
OrganizationGrant numberCountry
Other private2019 Netherlands
Other private2336 Netherlands
Agencia Estatal de Investigacion (AEI)PID2022-136322NB-I00 Spain
Other government34459European Union
Other government37638European Union
Other government68606European Union
CitationJournal: Sci Adv / Year: 2026
Title: High-resolution cryo-EM structure of integrin αIIbβ3 bound to disease-causing maternal HPA-1a antibody that blocks integrin activation.
Authors: José M de Pereda / Wendy Stam / Marcos Gragera / Femke van der Meer / Francisco J Chichón / Eleftherios Zarkadas / Ellen van der Schoot / Gestur Vidarsson / Junichi Takagi / Coert Margadant /
Abstract: Integrins promote immunity, embryonic development, wound healing, and hemostasis, and are activated by 'bent/closed' to 'extended/open' conformational changes. Integrin αIIbβ3, being crucial for ...Integrins promote immunity, embryonic development, wound healing, and hemostasis, and are activated by 'bent/closed' to 'extended/open' conformational changes. Integrin αIIbβ3, being crucial for platelet activation and aggregation, is a therapeutic target for bleeding disorders and thrombosis. Human Platelet Antigen-1a (HPA-1a) on β3 is recognized by pregnancy-associated maternal alloantibodies, potentially causing fetal/neonatal alloimmune thrombocytopenia (FNAIT) and even intracranial hemorrhage or perinatal death. We report the structure of an anti-HPA-1a antibody fragment (Fab 26.4) in complex with integrin αIIbβ3 at high resolution by cryo-electron microscopy. Fab 26.4 binding locks αIIbβ3 in the inactive, bent/closed conformation, is incompatible with integrin extension, and inhibits αIIbβ3-dependent fibrinogen binding and platelet aggregation. Thus, anti-HPA-1a antibodies directly impair integrin activation by preventing required conformational changes. These insights will improve FNAIT diagnostics and treatment, and spark the development of novel allosteric inhibitors against β3 integrins for future therapeutic applications.
History
DepositionNov 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-IIb
B: Integrin beta-3
H: Antibody 26.4 Fab heavy chain
L: Antibody 26.4 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,81118
Polymers239,3334
Non-polymers3,47814
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-IIb / GPalpha IIb / GPIIb / Platelet membrane glycoprotein IIb


Mass: 108456.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B, GP2B, ITGAB / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08514
#2: Protein Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 81402.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05106

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Antibody , 2 types, 2 molecules HL

#3: Antibody Antibody 26.4 Fab heavy chain


Mass: 26033.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Antibody 26.4 Fab light chain


Mass: 23441.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 4 types, 7 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 16 molecules

#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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

ComponentName: Complex of integrin aIIbb3 ectodomains bound to the Fab 26.4
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.24 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.5
Details: 50 mM Tris-HCl, 150 mM NaCl, 1 mM CaCl2, 1 mM MgCl2, pH 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris-HCl1
2150 mMsodium chlorideNaCl1
31 mMcalcium chlorideCaCl21
41 mMmagnesium chlorideMgCl21
SpecimenConc.: 0.13 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 25 mA / Grid material: COPPER/RHODIUM / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 94 % / Chamber temperature: 277 K / Details: blotting time 3 sec, blot force 3

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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 magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 2.93 sec. / Electron dose: 41.57 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1crYOLO1.9.9particle selection
2PHENIX2.0_5884model refinement
5cisTEM5.0.2CTF correction
10cryoSPARC4.6.2initial Euler assignment
12cryoSPARC4.6.2classification
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6717934
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84349 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Initial rigid body fitting of individual domains was done using Coot
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-IDSource nameType
13FCS

3fcs

A3FCSA1PDBexperimental model
23FCS

3fcs

B3FCSB1PDBexperimental model
3HAlphaFoldin silico model
4LAlphaFoldin silico model
RefinementHighest resolution: 2.64 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00713130
ELECTRON MICROSCOPYf_angle_d0.79317819
ELECTRON MICROSCOPYf_dihedral_angle_d10.1442100
ELECTRON MICROSCOPYf_chiral_restr0.0532001
ELECTRON MICROSCOPYf_plane_restr0.0052300

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