Structure of the Plexin Ectodomain Bound by Semaphorin-Mimicking Antibodies

Abstract

Semaphorin family proteins act on cells to mediate both repulsive and attractive guidance via binding to plexin family receptors, thereby playing fundamental roles in the morphogenesis and homeostasis of various tissues. Although semaphorin-plexin signaling is implicated in various diseases and is thus a target of intensive research, our mechanistic understanding of how semaphorins activate plexins on the cell surface is limited. Here, we describe unique anti-plexin-A1 antibodies that can induce a collapsed morphology in mouse dendritic cells as efficiently as the semaphorin 3A (Sema3A) ligand. Precise epitope analysis indicates that these “semaphorin-mimicking” antibodies dimerize cell-surface plexin-A1 by binding to the N-terminal sema domain of the plexin at sites away from the interface used by the Sema3A ligand. Structural analysis of plexin-A1 fragments using negative stain electron microscopy further revealed that this agonistic capacity is closely linked to the location and orientation of antibody binding. In addition, the full-length plexin-A1 ectodomain exhibited a highly curved “C” shape, reinforcing the very unusual dimeric receptor conformation of this protein at the cell surface when engaged with Sema3A or agonistic antibodies.

Allosteric Inhibition of a Semaphorin 4D Receptor Plexin B1 by a High-Affinity Macrocyclic Peptide

“…It is generally believed that semaphorin-induced plexin dimerization is the key event during the cell signaling. Very recently, we and others (Suzuki et al, 2016;Kong et al, 2016) have discovered that the entire plexin ectodomain assumes a highly unusual ''C-shape,'' and suggested that a particular type of plexin dimer arrangement can elicit a positive signal. It is therefore possible that binding of PB1m6 may not only modulate the ligand affinity but also regulate the conformation of the entire PlxnB1 ectodomain on the cell surface, resulting in an efficient signal suppression.…”

Cryo-EM structure of the PlexinC1/A39R complex reveals inter-domain interactions critical for ligand-induced activation

“…Recent structural studies of the intact extracellular region of class A plexins in the apo state show that the three PSI domains and six IPT domains together adopt a highly curled shape, leading to an overall ringlike architecture 14,15 . Based on these structures, a docking model of the entire extracellular region of class A plexins in complex with semaphorin has been constructed, showing that the ring-shape of plexin brings the two copies of the membrane-proximal IPT6 domain in the dimeric complex to close proximity, compatible with the formation of the intracellular active dimer 14,15 . Classes B and D plexins may use the same mechanism, as their extracellular regions have the same domain composition as class A plexins.…”

Mechanochemical control of epidermal stem cell divisions by B-plexins

“…The extracellular domain of several plexins has been shown to adopt different conformations ranging from a nearly closed, ring-like form to a more-open, chair-like form 17,47,48 . Very recently, a particular plexin, Plexin-D1, has been reported to sense shear stress-induced mechanical forces in endothelial cells 17 .…”