3ZDY

Integrin alphaIIB beta3 headpiece and RGD peptide complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history. 


Literature

Complete Integrin Headpiece Opening in Eight Steps.

Zhu, J., Zhu, J., Springer, T.A.

(2013) J Cell Biol 201: 1053

  • DOI: 10.1083/jcb.201212037
  • Primary Citation of Related Structures:  
    3ZDX, 3ZDY, 3ZDZ, 3ZE0, 3ZE1, 3ZE2

  • PubMed Abstract: 

    • Carefully soaking crystals with Arg-Gly-Asp (RGD) peptides, we captured eight distinct RGD-bound conformations of the αIIbβ3 integrin headpiece. Starting from the closed βI domain conformation, we saw six intermediate βI conformations and finally the fully open βI with the hybrid domain swung out in the crystal lattice ...

    Carefully soaking crystals with Arg-Gly-Asp (RGD) peptides, we captured eight distinct RGD-bound conformations of the αIIbβ3 integrin headpiece. Starting from the closed βI domain conformation, we saw six intermediate βI conformations and finally the fully open βI with the hybrid domain swung out in the crystal lattice. The β1-α1 backbone that hydrogen bonds to the Asp side chain of RGD was the first element to move followed by adjacent to metal ion-dependent adhesion site Ca(2+), α1 helix, α1' helix, β6-α7 loop, α7 helix, and hybrid domain. We define in atomic detail how conformational change was transmitted over long distances in integrins, 40 Å from the ligand binding site to the opposite end of the βI domain and 80 Å to the far end of the hybrid domain. During these movements, RGD slid in its binding groove toward αIIb, and its Arg side chain became ordered. RGD concentration requirements in soaking suggested a >200-fold higher affinity after opening. The thermodynamic cycle shows how higher affinity pays the energetic cost of opening.

    Organizational Affiliation: 

    Department of Biological Chemistry and Molecular Pharmacology, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INTEGRIN ALPHA-IIBA, C457Homo sapiensMutation(s): 0 
Gene Names: ITGA2B, GP2B, ITGAB
Find proteins for P08514 (Homo sapiens)
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Go to UniProtKB:  P08514
NIH Common Fund Data Resources
PHAROS:  P08514
GTEx:  ENSG00000005961
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
INTEGRIN BETA-3B, D472Homo sapiensMutation(s): 0 
Gene Names: ITGB3, GP3A
Find proteins for P05106 (Homo sapiens)
Explore P05106 
Go to UniProtKB:  P05106
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PHAROS:  P05106
GTEx:  ENSG00000259207
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
10E5 FAB HEAVY CHAINE, G [auth H]221Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
10E5 FAB LIGHT CHAINF, J [auth L]214Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RGD PEPTIDEH [auth I], I [auth J]6Homo sapiensMutation(s): 0 
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Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth G], M4 N-Glycosylation Oligosaccharides Interaction
Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth K], N2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
 HA [auth B], VA [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
SO4
Query on SO4
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BA [auth B] , CA [auth B] , DA [auth B] , IA [auth C] , JA [auth C] , KA [auth C] , LA [auth C] , MA [auth C] , 
BA [auth B],  CA [auth B],  DA [auth B],  IA [auth C],  JA [auth C],  KA [auth C],  LA [auth C],  MA [auth C],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  RA [auth D],  S [auth A],  T [auth A],  U [auth A],  V [auth A],  W [auth A],  WA [auth L],  XA [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
CA
Query on CA
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AA [auth A] , FA [auth B] , GA [auth B] , NA [auth C] , OA [auth C] , PA [auth C] , QA [auth C] , TA [auth D] , 
AA [auth A],  FA [auth B],  GA [auth B],  NA [auth C],  OA [auth C],  PA [auth C],  QA [auth C],  TA [auth D],  UA [auth D],  X [auth A],  Y [auth A],  Z [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
 EA [auth B], SA [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 257.76α = 90
b = 145.25β = 90
c = 106.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 2.0: 2017-10-25
    Changes: Advisory, Atomic model, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary