The receptor VLDLR binds East Equine Encephalitis virus through multiple distinct modes

Eastern Equine Encephalitis virus (EEEV) is an alphavirus that can cause severe diseases in infected humans. The very low-density lipoprotein receptor (VLDLR) was recently identified as a receptor of EEEV. Herein, we performed cryo-electron microscopy structural and biochemistry studies on the specific interactions between EEEV and VLDLR. Our results show that VLDLR binds EEEV at three different sites A, B and C through its membrane-distal 8 LDLR class A (LA) repeats (LA1-8). Site A is located in the cleft in between the E1-E2 heterodimers of the surface trimeric spikes. Site B is located near the connecting {beta} ribbon in between the B and A-C domains of E2 and is in proximity to site A, while site C is on the domain B of E2. LA1 and LA5 specifically recognize site A, whereas LA2, LA3 and LA6 can bind both sites A and C. The binding of VLDLR LAs to EEEV is in complex modes. The LA1-2 mediated binding plays a critical role in mediating virus entry. The mutation W132G of VLDLR impairs the binding of LA3, drives the switch of the binding modes, and significantly enhances the attachment of EEEV to the cell. The W132G variant of VLDLR could be identified in human genome and SNP sequences, implying that people with similar mutations in VLDLR may be highly susceptible to EEEV infection.