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- PDB-11yb: Structure of AlphaIIbBeta3-R21C11 Fab in the near-bent conformation -

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Basic information

Entry
Database: PDB / ID: 11yb
TitleStructure of AlphaIIbBeta3-R21C11 Fab in the near-bent conformation
Components
  • Integrin alpha-IIb
  • Integrin beta-3
  • R21C11 Fab heavy chain
  • R21C11 Fab light chain
KeywordsBLOOD CLOTTING / Monoclonal antibody / integrin receptor / platelets / inhibiter of PDI binding to AlphaIIbbeta3 integrin
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 / glycinergic synapse / 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 / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / cell adhesion mediated by integrin / negative chemotaxis / positive regulation of osteoblast proliferation / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / cellular response to insulin-like growth factor stimulus / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / regulation of postsynaptic neurotransmitter receptor internalization / 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 / 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 / positive regulation of smooth muscle cell proliferation / positive regulation of endothelial cell migration / cell adhesion molecule binding / integrin-mediated signaling pathway / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / response to activity / protein kinase C binding / wound healing / Signal transduction by L1 / cellular response to xenobiotic stimulus / regulation of actin cytoskeleton organization / cell-cell adhesion / cellular response to mechanical stimulus / platelet activation / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet aggregation / VEGFA-VEGFR2 Pathway / integrin binding / ruffle membrane / blood coagulation / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction
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. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2.
Similarity search - Domain/homology
Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang, J.L. / Coller, B. / Wang, L. / Li, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5R01HL019278-48 United States
CitationJournal: Blood Adv / Year: 2026
Title: A monoclonal antibody to platelet αIIbβ3 that inhibits protein disulfide isomerase binding and platelet aggregation.
Authors: Lu Wang / Jialing Wang / Jihong Li / Barry S Coller /
Abstract: Platelet integrin αIIbβ3 plays a pivotal role in hemostasis and thrombosis. Protein disulfide isomerase (PDI) binds to αIIbβ3 and mediates its activation. The binding region(s) on αIIbβ3 for ...Platelet integrin αIIbβ3 plays a pivotal role in hemostasis and thrombosis. Protein disulfide isomerase (PDI) binds to αIIbβ3 and mediates its activation. The binding region(s) on αIIbβ3 for PDI remains to be established. We identified a new anti-αIIbβ3 murine monoclonal antibody, R21C11, that inhibits PDI binding to platelets, ligand binding to αIIbβ3, and platelet aggregation. R21C11 inhibited recombinant PDI binding to platelets activated with the PAR1 thrombin receptor activating peptide SFLLRN (T6). Reciprocally, PDI partially reduced R21C11 binding to platelets. PDI was translocated to the platelet surface after activation and activated platelets showed higher PDI reductase activity. R211C11 decreased both the amount of PDI and the reductase activity. R21C11 partially inhibited both fibrinogen and PAC-1 binding to αIIbβ3 and platelet aggregation induced by ADP and T6. R21C11 bound slowly to unactivated platelets and more rapidly after T6 activation; eptifibatide, which induces the αIIbβ3 extended-open conformation, also increased the speed of R21C11 binding. Activation also increased total R21C11 binding. Cryogenic electron microscopy single-particle analysis of the R21C11 Fab-αIIbβ3 complex revealed that R21C11 binds to the β3 β-tail domain in both nearly bent and semiextended-closed conformations of αIIbβ3. R21C11 Fab clashed with the β3 β-I domain in the fully bent conformation, accounting for the slow binding rate of R21C11. These data are consistent with R21C11 inhibiting PDI binding by steric hindrance and the activation dependence of PDI binding. Taken together, these data suggest that the β-tail domain and/or neighboring area is the binding site for PDI on integrin αIIbβ3.
History
DepositionMar 17, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 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: R21C11 Fab heavy chain
L: R21C11 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,08412
Polymers247,7794
Non-polymers3058
Water00
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: 113477.523 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: Homo sapiens (human) / References: UniProt: P08514
#2: Protein Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 87150.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Production host: Homo sapiens (human) / References: UniProt: P05106

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Antibody , 2 types, 2 molecules HL

#3: Antibody R21C11 Fab heavy chain


Mass: 23931.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Antibody R21C11 Fab light chain


Mass: 23218.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LLTQSPATLSVTPGETVSLSCRASQSIYKNLHWYQQKSHRSPSLLIKSASESISGIPSRFTGSGSGTDYILSINSVEPEDEGIYYCLQGYSIPFTFGAGSKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDLNVKWKLDGSERQNGVLDSWTDQDSKDSTYMSSTLTLTKDEYERHNSYTCEATHKTSTSPLVKSFNRNEC
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Non-polymers , 2 types, 8 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
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
1The structure of AlphaIIbBeta3-R21C11 Fab in the near-bent conformationCOMPLEX#1-#40NATURAL
2Integrin AlphaIIbbeta3COMPLEX#1-#21NATURAL
3R21C11 FabCOMPLEX#3-#41NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.25 MDaYES
210.2 MDaNO
310.05 MDaNO
43
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Mus musculus (house mouse)10090
Buffer solutionpH: 7.4
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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
4cryoSPARCv4.4.0CTF correction
7UCSF Chimeraversion 1.16model fitting
9cryoSPARCv4.4.0initial Euler assignment
10cryoSPARCv4.4.0final Euler assignment
11cryoSPARCv4.4.0classification
12cryoSPARCv4.4.03D reconstruction
13PHENIXversion 1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1332000
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49648 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-ID
18T2V

8t2v

A8T2VA
28T2V

8t2v

B8T2VB
37LA4

7la4

H7LA4H2
47LA4

7la4

L7LA4L2

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