3ZDX

Integrin alphaIIB beta3 headpiece and RGD peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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 ...

    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 LengthOrganismDetails
INTEGRIN ALPHA-IIBA, C457Homo sapiensMutation(s): 0 
Gene Names: ITGA2BGP2BITGAB
Find proteins for P08514 (Homo sapiens)
Explore P08514 
Go to UniProtKB:  P08514
NIH Common Fund Data Resources
PHAROS  P08514
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INTEGRIN BETA-3B, D472Homo sapiensMutation(s): 0 
Gene Names: ITGB3GP3A
Find proteins for P05106 (Homo sapiens)
Explore P05106 
Go to UniProtKB:  P05106
NIH Common Fund Data Resources
PHAROS  P05106
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
10E5 FAB, HEAVY CHAINE, H221Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
10E5 FAB, LIGHT CHAINF, L214Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
5 N-Glycosylation
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, K
2 N-Glycosylation
Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation
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-glucopyranose
J
4 N-Glycosylation
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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B, 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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A, C, D, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, B, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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B, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 259.71α = 90
b = 144.96β = 90
c = 104.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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