3QA3 image
Deposition Date 2011-01-10
Release Date 2011-11-30
Last Version Date 2024-10-09
Entry Detail
PDB ID:
3QA3
Title:
Crystal Structure of A-domain in complex with antibody
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Mus musculus (Taxon ID: 10090)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Antibody Light chain
Chain IDs:A (auth: C), D (auth: A), G (auth: F), J
Chain Length:220
Number of Molecules:4
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Antibody Heavy chain
Chain IDs:B (auth: D), E (auth: B), H, K
Chain Length:224
Number of Molecules:4
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:Integrin alpha-M
Gene (Uniprot):ITGAM
Mutations:I316G
Chain IDs:C (auth: G), F (auth: E), I, L
Chain Length:190
Number of Molecules:4
Biological Source:Homo sapiens
Primary Citation
Stable Coordination of the Inhibitory Ca2+ Ion at the Metal Ion-Dependent Adhesion Site in Integrin CD11b/CD18 by an Antibody-Derived Ligand Aspartate: Implications for Integrin Regulation and Structure-Based Drug Design.
J.Immunol. 187 6393 6401 (2011)
PMID: 22095715 DOI: 10.4049/jimmunol.1102394

Abstact

A central feature of integrin interaction with physiologic ligands is the monodentate binding of a ligand carboxylate to a Mg(2+) ion hexacoordinated at the metal ion-dependent adhesion site (MIDAS) in the integrin A domain. This interaction stabilizes the A domain in the high-affinity state, which is distinguished from the default low-affinity state by tertiary changes in the domain that culminate in cell adhesion. Small molecule ligand-mimetic integrin antagonists act as partial agonists, eliciting similar activating conformational changes in the A domain, which has contributed to paradoxical adhesion and increased patient mortality in large clinical trials. As with other ligand-mimetic integrin antagonists, the function-blocking mAb 107 binds MIDAS of integrin CD11b/CD18 A domain (CD11bA), but in contrast, it favors the inhibitory Ca(2+) ion over the Mg(2+) ion at MIDAS. We determined the crystal structures of the Fab fragment of mAb 107 complexed to the low- and high-affinity states of CD11bA. Favored binding of the Ca(2+) ion at MIDAS is caused by the unusual symmetric bidentate ligation of a Fab-derived ligand Asp to a heptacoordinated MIDAS Ca(2+) ion. Binding of the Fab fragment of mAb 107 to CD11bA did not trigger the activating tertiary changes in the domain or in the full-length integrin. These data show that the denticity of the ligand Asp/Glu can modify the divalent cation selectivity at MIDAS and hence integrin function. Stabilizing the Ca(2+) ion at MIDAS by bidentate ligation to a ligand Asp/Glu may provide one approach for designing pure integrin antagonists.

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