2VDN

Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Eptifibatide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report



Literature

Structural Basis for Distinctive Recognition of Fibrinogen Gammac Peptide by the Platelet Integrin Alphaiibbeta3.

Springer, T.A., Zhu, J., Xiao, T.

(2008) J Cell Biol 182: 791

  • DOI: 10.1083/jcb.200801146
  • Primary Citation of Related Structures:  
    2VC2, 2VDP, 2VDQ, 2VDR, 2VDK, 2VDL, 2VDM, 2VDN, 2VDO

  • PubMed Abstract: 

    • Hemostasis and thrombosis (blood clotting) involve fibrinogen binding to integrin alpha(IIb)beta(3) on platelets, resulting in platelet aggregation. alpha(v)beta(3) binds fibrinogen via an Arg-Asp-Gly (RGD) motif in fibrinogen's alpha subunit. alpha(IIb) ...

    Hemostasis and thrombosis (blood clotting) involve fibrinogen binding to integrin alpha(IIb)beta(3) on platelets, resulting in platelet aggregation. alpha(v)beta(3) binds fibrinogen via an Arg-Asp-Gly (RGD) motif in fibrinogen's alpha subunit. alpha(IIb)beta(3) also binds to fibrinogen; however, it does so via an unstructured RGD-lacking C-terminal region of the gamma subunit (gammaC peptide). These distinct modes of fibrinogen binding enable alpha(IIb)beta(3) and alpha(v)beta(3) to function cooperatively in hemostasis. In this study, crystal structures reveal the integrin alpha(IIb)beta(3)-gammaC peptide interface, and, for comparison, integrin alpha(IIb)beta(3) bound to a lamprey gammaC primordial RGD motif. Compared with RGD, the GAKQAGDV motif in gammaC adopts a different backbone configuration and binds over a more extended region. The integrin metal ion-dependent adhesion site (MIDAS) Mg(2+) ion binds the gammaC Asp side chain. The adjacent to MIDAS (ADMIDAS) Ca(2+) ion binds the gammaC C terminus, revealing a contribution for ADMIDAS in ligand binding. Structural data from this natively disordered gammaC peptide enhances our understanding of the involvement of gammaC peptide and integrin alpha(IIb)beta(3) in hemostasis and thrombosis.

    Related Citations: 
    • Structural Basis for Allostery in Integrins and Binding to Fibrinogen-Mimetic Therapeutics
      Xiao, T., Takagi, J., Coller, B.S., Wang, J.-H., Springer, T.A.
      (2004) Nature 432: 59
    Organizational Affiliation: 

    Department of Pathology, Immune Disease Institute, Harvard Medical School, Boston, MA 02115, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INTEGRIN ALPHA-IIB A452Homo sapiensMutation(s): 0 
Gene Names: ITGA2B, GP2B, ITGAB
Find proteins for P08514 (Homo sapiens)
Explore P08514 
Go to UniProtKB:  P08514
NIH Common Fund Data Resources
PHAROS:  P08514
GTEx:  ENSG00000005961
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
INTEGRIN BETA-3 B461Homo sapiensMutation(s): 0 
Gene Names: ITGB3, GP3A
Find proteins for P05106 (Homo sapiens)
Explore P05106 
Go to UniProtKB:  P05106
NIH Common Fund Data Resources
PHAROS:  P05106
GTEx:  ENSG00000259207
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
EPTIFIBATIDE C8synthetic constructMutation(s): 0 
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(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN H221Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN L214Mus musculusMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
5 N-Glycosylation Oligosaccharides Interaction
Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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
E
7 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.593α = 90
b = 149.593β = 90
c = 175.683γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2016-12-28
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-11-20
    Changes: Advisory, Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary