4Z7Q: Integrin alphaIIbbeta3 in complex with AGDV-NH2 peptide

Citation:
Abstract
The platelet integrin alphaIIbbeta3 binds to a KQAGDV motif at the fibrinogen gamma-chain C terminus and to RGD motifs present in loops in many extracellular matrix proteins. These ligands bind in a groove between the integrin alpha and beta-subunits; the basic Lys or Arg side chain hydrogen bonds to the alphaIIb-subunit, and the acidic Asp side chain coordinates to a metal ion held by the beta3-subunit. Ligand binding induces headpiece opening, with conformational change in the beta-subunit. During this opening, RGD slides in the ligand-binding pocket toward alphaIIb, with movement of the betaI-domain beta1-alpha1 loop toward alphaIIb, enabling formation of direct, charged hydrogen bonds between the Arg side chain and alphaIIb. Here we test whether ligand interactions with beta3 suffice for stable ligand binding and headpiece opening. We find that the AGDV tetrapeptide from KQAGDV binds to the alphaIIbbeta3 headpiece with affinity comparable with the RGDSP peptide from fibronectin. AGDV induced complete headpiece opening in solution as shown by increase in hydrodynamic radius. Soaking of AGDV into closed alphaIIbbeta3 headpiece crystals induced intermediate states similarly to RGDSP. AGDV has very little contact with the alpha-subunit. Furthermore, as measured by epitope exposure, AGDV, like the fibrinogen gamma C-terminal peptide and RGD, caused integrin extension on the cell surface. Thus, pushing by the beta3-subunit on Asp is sufficient for headpiece opening and ligand sliding, and no pulling by the alphaIIb subunit on Arg is required.
PDB ID: 4Z7QDownload
MMDB ID: 134815
PDB Deposition Date: 2015/4/7
Updated in MMDB: 2015/12
Experimental Method:
x-ray diffraction
Resolution: 2.7  Å
Source Organism:
Mus musculus
Similar Structures:
Biological Unit for 4Z7Q: hexameric; determined by author
Molecular Components in 4Z7Q
Label Count Molecule
Proteins (6 molecules)
1
Integrin Alpha-iib(Gene symbol: ITGA2B)
Molecule annotation
1
Integrin Beta-3(Gene symbol: ITGB3)
Molecule annotation
1
Monoclonal Antibody 10e5 Heavy Chain
Molecule annotation
1
Monoclonal Antibody 10e5 Light Chain
Molecule annotation
2
Tetrapeptide Agdv-nh2
Molecule annotation
Chemicals (18 molecules)
1
4
2
4
3
1
4
4
5
4
6
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.