7P2D image
Entry Detail
PDB ID:
7P2D
Keywords:
Title:
Structure of alphaMbeta2/Cd11bCD18 headpiece in complex with a nanobody
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2021-07-05
Release Date:
2022-05-04
Method Details:
Experimental Method:
Resolution:
3.20 Å
R-Value Free:
0.29
R-Value Work:
0.26
R-Value Observed:
0.26
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Isoform 2 of Integrin alpha-M
Chain IDs:A
Chain Length:763
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Integrin beta
Chain IDs:B
Chain Length:473
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:hCD11bNb1 nanobody
Chain IDs:C
Chain Length:129
Number of Molecules:1
Biological Source:Lama glama
Primary Citation
Structural insights into the function-modulating effects of nanobody binding to the integrin receptor alpha M beta 2.
J.Biol.Chem. 298 102168 102168 (2022)
PMID: 35738398 DOI: 10.1016/j.jbc.2022.102168

Abstact

The integrin receptor αMβ2 mediates phagocytosis of complement-opsonized objects, adhesion to the extracellular matrix, and transendothelial migration of leukocytes. However, the mechanistic aspects of αMβ2 signaling upon ligand binding are unclear. Here, we present the first atomic structure of the human αMβ2 headpiece fragment in complex with the nanobody (Nb) hCD11bNb1 at a resolution of 3.2 Å. We show that the receptor headpiece adopts the closed conformation expected to exhibit low ligand affinity. The crystal structure indicates that in the R77H αM variant, associated with systemic lupus erythematosus, the modified allosteric relationship between ligand binding and integrin outside-inside signaling is due to subtle conformational effects transmitted over a distance of 40 Å. Furthermore, we found the Nb binds to the αI domain of the αM subunit in an Mg2+-independent manner with low nanomolar affinity. Biochemical and biophysical experiments with purified proteins demonstrated that the Nb acts as a competitive inhibitor through steric hindrance exerted on the thioester domain of complement component iC3b attempting to bind the αM subunit. Surprisingly, we show that the Nb stimulates the interaction of cell-bound αMβ2 with iC3b, suggesting that it may represent a novel high-affinity proteinaceous αMβ2-specific agonist. Taken together, our data suggest that the iC3b-αMβ2 complex may be more dynamic than predicted from the crystal structure of the core complex. We propose a model based on the conformational spectrum of the receptor to reconcile these observations regarding the functional consequences of hCD11bNb1 binding to αMβ2.

Legend

Protein

Chemical

Disease

Primary Citation of related structures