Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly

ABSTRACT: M is the most abundant structural membrane protein in coronaviruses and is essential for the formation of infectious virus particles. SARS-CoV-2 M adopts two conformations, Mshort and Mlong, and regulated transition between states is hypothesized to coordinate viral assembly and budding. However, the factors that regulate M conformation and roles for each state are unknown. Here, we discover a direct M-sphingolipid interaction that controls M conformational dynamics, interaction with other structural proteins, and virus assembly. We show M binds Golgi-enriched anionic lipids including ceramide-1-phosphate (C1P). Molecular dynamics simulations show C1P interaction promotes a long to short transition and energetically stabilizes Mshort. Cryo-EM structures show C1P specifically binds Mshort at a conserved site bridging transmembrane and cytoplasmic regions. Hydrogen-deuterium exchange mass spectrometry confirms that C1P binds primarily to a condensed Mshort conformation and shows a switching from Mshort to Mlong in virus-like particles. Disrupting Mshort-C1P interaction alters M subcellular localization, reduces colocalization with Spike and E, and reduces virus-like particle formation and cell entry. Together, these results show endogenous signaling lipids regulate M structure and support a model in which Mshort is stabilized in the early endomembrane system to organize other structural proteins prior to viral budding.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Severe Acute Respiratory Syndrome Coronavirus 2

SUBMITTER: Sean Braet  

LAB HEAD: Dr. Ganesh S. Anand

PROVIDER: PXD079401 | Pride | 2026-07-09

REPOSITORIES: Pride