6V4P

Structure of the integrin AlphaIIbBeta3-Abciximab complex


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 1.3 of the entry. See complete history


Literature

Cryo-Electron Microscopy Structure of the alpha IIb beta 3-Abciximab Complex.

Nesic, D.Zhang, Y.Spasic, A.Li, J.Provasi, D.Filizola, M.Walz, T.Coller, B.S.

(2020) Arterioscler Thromb Vasc Biol 40: 624-637

  • DOI: 10.1161/ATVBAHA.119.313671
  • Primary Citation of Related Structures:  
    6V4P

  • PubMed Abstract: 
  • The αIIbβ3 antagonist antiplatelet drug abciximab is the chimeric antigen-binding fragment comprising the variable regions of murine monoclonal antibody 7E3 and the constant domains of human IgG1 and light chain κ. Previous mutagenesis studies suggested that abciximab binds to the β3 C177-C184 specificity-determining loop (SDL) and Trp129 on the adjacent β1-α1 helix ...

    The αIIbβ3 antagonist antiplatelet drug abciximab is the chimeric antigen-binding fragment comprising the variable regions of murine monoclonal antibody 7E3 and the constant domains of human IgG1 and light chain κ. Previous mutagenesis studies suggested that abciximab binds to the β3 C177-C184 specificity-determining loop (SDL) and Trp129 on the adjacent β1-α1 helix. These studies could not, however, assess whether 7E3 or abciximab prevents fibrinogen binding by steric interference, disruption of either the αIIbβ3-binding pocket for fibrinogen or the β3 SDL (which is not part of the binding pocket but affects fibrinogen binding), or some combination of these effects. To address this gap, we used cryo-electron microscopy to determine the structure of the αIIbβ3-abciximab complex at 2.8 Å resolution. Approach and Results: The interacting surface of abciximab is comprised of residues from all 3 complementarity-determining regions of both the light and heavy chains, with high representation of aromatic residues. Binding is primarily to the β3 SDL and neighboring residues, the β1-α1 helix, and β3 residues Ser211, Val212 and Met335. Unexpectedly, the structure also indicated several interactions with αIIb. As judged by the cryo-electron microscopy model, molecular-dynamics simulations, and mutagenesis, the binding of abciximab does not appear to rely on the interaction with the αIIb residues and does not result in disruption of the fibrinogen-binding pocket; it does, however, compress and reduce the flexibility of the SDL.


    Organizational Affiliation

    From the Allen and Frances Adler Laboratory of Blood and Vascular Biology (D.N., J.L., B.S.C.), Rockefeller University, NY.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin alpha-IIbA963Homo sapiensMutation(s): 0 
Gene Names: ITGA2BGP2BITGAB
UniProt & NIH Common Fund Data Resources
Find proteins for P08514 (Homo sapiens)
Explore P08514 
Go to UniProtKB:  P08514
PHAROS:  P08514
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UniProt GroupP08514
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin beta-3B690Homo sapiensMutation(s): 0 
Gene Names: ITGB3GP3A
UniProt & NIH Common Fund Data Resources
Find proteins for P05106 (Homo sapiens)
Explore P05106 
Go to UniProtKB:  P05106
PHAROS:  P05106
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UniProt GroupP05106
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Abciximab, heavy chainC225synthetic constructMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Abciximab, light chainD214synthetic constructMutation(s): 0 
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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 StatesHL19278
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United StatesUL1 TR001866
National Science Foundation (NSF, United States)United StatesACI-1053575

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-02-12
    Changes: Source and taxonomy
  • Version 1.2: 2020-03-04
    Changes: Database references
  • Version 1.3: 2020-03-11
    Changes: Database references