9DAO | pdb_00009dao

AlphaIIbbeta3 in fully-extended conformation in complex with R6H8 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An alpha IIb beta 3 ligand-mimetic murine monoclonal antibody that produces platelet activation by engaging the Fc gamma IIa receptor.

Wang, J.Buitrago, L.Wang, L.Li, J.Walz, T.Coller, B.S.

(2025) Blood Adv 9: 3518-3529

  • DOI: https://doi.org/10.1182/bloodadvances.2024015368
  • Primary Citation of Related Structures:  
    9DAO, 9DAX

  • PubMed Abstract: 

    To produce a murine monoclonal antibody that binds to αIIbβ3 and inhibits clot retraction (CR) we immunized mice with human platelets and tested hybridoma supernatants for their ability to bind to αIIbβ3 and inhibit CR. The IgG1 mAb R6H8 completely inhibited CR at 20 µg/ml. Paradoxically, 5 µg/ml R6H8 initiated platelet aggregation and induced P-selectin expression, fibrinogen binding, and PAC-1 binding. At 20 µg/ml, however, R6H8 completely inhibited aggregation induced by peptide SFLLRN (25 µg/ml; T6) and T6-induced fibrinogen and PAC-1 binding to platelets. Platelet aggregation induced by R6H8 was inhibited by mAb IV.3, which blocks the FcγIIa receptor (FcγRIIa), and the Fab fragment of R6H8 did not induce platelet aggregation, suggesting that R6H8 binds to both αIIbβ3 and FcγRIIa. Cryo-EM analysis of the R6H8 Fab-αIIbβ3 complex revealed that R6H8: 1) Binds to the αIIbβ3 RGD binding pocket via an RYD sequence in its heavy chain CDR3, 2) Interacts with β3 Asp126, producing a reorientation of Asp126 and loss of the ADMIDAS Ca2+, and 3) Initiates swing-out of the β3 hybrid domain. We conclude that R6H8 is an αIIbβ3 ligand-mimetic mAb that activates platelets via FcγRIIa at low concentrations and potently inhibits platelet aggregation and clot retraction at high concentrations. R6H8 simulates the actions of a number of pathological antibodies, including platelet-activating antibodies developed after therapy with glycoprotein IIb/IIIa (αIIbβ3) inhibitors and platelet-activating antibodies in heparin-induced thrombocytopenia and vaccine-induced immune thrombotic thrombocytopenia. As such, it may be a valuable reagent for better understanding these disorders and identifying potential therapies.


  • Organizational Affiliation
    • The Rockefeller University, NEW YORK, New York, United States.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-IIb1,008Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P08514 (Homo sapiens)
Explore P08514 
Go to UniProtKB:  P08514
PHAROS:  P08514
GTEx:  ENSG00000005961 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08514
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin beta-3762Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05106 (Homo sapiens)
Explore P05106 
Go to UniProtKB:  P05106
PHAROS:  P05106
GTEx:  ENSG00000259207 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05106
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
R6H8 Fab heavy chainC [auth H]227Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
R6H8 Fab light chainD [auth L]214Mus musculusMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States5R01HL019278-48

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection, Database references