Architecture of the Sema3A/PlexinA4/Neuropilin tripartite complex

Defen Lu, Guijun Shang, Xiaojing He, Xiao-chen Bai () and Xuewu Zhang ()
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Defen Lu: University of Texas Southwestern Medical Center
Guijun Shang: University of Texas Southwestern Medical Center
Xiaojing He: College of Life Science and Technology, Huazhong University of Science and Technology
Xiao-chen Bai: University of Texas Southwestern Medical Center
Xuewu Zhang: University of Texas Southwestern Medical Center

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: Abstract Secreted class 3 semaphorins (Sema3s) form tripartite complexes with the plexin receptor and neuropilin coreceptor, which are both transmembrane proteins that together mediate semaphorin signal for neuronal axon guidance and other processes. Despite extensive investigations, the overall architecture of and the molecular interactions in the Sema3/plexin/neuropilin complex are incompletely understood. Here we present the cryo-EM structure of a near intact extracellular region complex of Sema3A, PlexinA4 and Neuropilin 1 (Nrp1) at 3.7 Å resolution. The structure shows a large symmetric 2:2:2 assembly in which each subunit makes multiple interactions with others. The two PlexinA4 molecules in the complex do not interact directly, but their membrane proximal regions are close to each other and poised to promote the formation of the intracellular active dimer for signaling. The structure reveals a previously unknown interface between the a2b1b2 module in Nrp1 and the Sema domain of Sema3A. This interaction places the a2b1b2 module at the top of the complex, far away from the plasma membrane where the transmembrane regions of Nrp1 and PlexinA4 embed. As a result, the region following the a2b1b2 module in Nrp1 must span a large distance to allow the connection to the transmembrane region, suggesting an essential role for the long non-conserved linkers and the MAM domain in neuropilin in the semaphorin/plexin/neuropilin complex.

Date: 2021
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DOI: 10.1038/s41467-021-23541-x

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