7NP9

Structure of the human CR3 - CD11bCD18 specific nanobody hCR3Nb1

Summary for 7NP9

• Entry DOI: 10.2210/pdb7np9/pdb
• Descriptor: hCR3Nb1, SULFATE ION (3 entities in total)
• Functional Keywords: nanobody, antibody, integrin receptor, complement, phagocytosis, inhibitor, immune system
• Biological source: Lama glama
• Total number of polymer chains: 1
• Total formula weight: 14319.88

Authors

Jensen, R.K.,Andersen, G.R. (deposition date: 2021-02-26, release date: 2022-03-23, Last modification date: 2024-02-07)

Primary citation

Jensen, R.K.,Pedersen, H.,Lorentzen, J.,Laursen, N.S.,Vorup-Jensen, T.,Andersen, G.R.
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

PubMed Abstract: The integrin receptor αβ mediates phagocytosis of complement-opsonized objects, adhesion to the extracellular matrix, and transendothelial migration of leukocytes. However, the mechanistic aspects of αβ signaling upon ligand binding are unclear. Here, we present the first atomic structure of the human αβ 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 α 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 α subunit in an Mg-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 α subunit. Surprisingly, we show that the Nb stimulates the interaction of cell-bound αβ with iC3b, suggesting that it may represent a novel high-affinity proteinaceous αβ-specific agonist. Taken together, our data suggest that the iC3b-αβ 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 αβ.

PubMed: 35738398
DOI: 10.1016/j.jbc.2022.102168

Experimental method

X-RAY DIFFRACTION (1.14 Å)