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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 / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization ...regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of bone resorption / platelet-derived growth factor receptor binding / mesodermal cell differentiation / glycinergic synapse / filopodium membrane / extracellular matrix binding / regulation of release of sequestered calcium ion into cytosol / positive regulation of cell adhesion mediated by integrin / apolipoprotein A-I-mediated signaling pathway / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / negative regulation of low-density lipoprotein particle clearance / angiogenesis involved in wound healing / wound healing, spreading of epidermal cells / positive regulation of leukocyte migration / apoptotic cell clearance / positive regulation of fibroblast migration / integrin complex / cell adhesion mediated by integrin / smooth muscle cell migration / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / positive regulation of smooth muscle cell migration / negative chemotaxis / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Syndecan interactions / positive regulation of cell-matrix adhesion / p130Cas linkage to MAPK signaling for integrins / regulation of postsynaptic neurotransmitter receptor internalization / cellular response to insulin-like growth factor stimulus / positive regulation of osteoblast proliferation / protein disulfide isomerase activity / microvillus membrane / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / TGF-beta receptor signaling activates SMADs / lamellipodium membrane / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / blood coagulation, fibrin clot formation / ECM proteoglycans / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / positive regulation of T cell migration / coreceptor activity / cellular response to platelet-derived growth factor stimulus / Integrin signaling / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / embryo implantation / cell adhesion molecule binding / positive regulation of endothelial cell migration / positive regulation of smooth muscle cell proliferation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / protein kinase C binding / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / wound healing / cellular response to mechanical stimulus / cell-cell adhesion / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet activation / VEGFA-VEGFR2 Pathway / platelet aggregation / integrin binding / cellular response to xenobiotic stimulus / positive regulation of fibroblast proliferation / ruffle membrane
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / 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 / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2.
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: To Be Published
Title: High-resolution cryo-EM structure of integrin aIIbb3 in complex with a disease-causing maternal HPA-1a antibody that blocks integrin activation
Authors: de 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.
History
DepositionNov 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: 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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