The SARS-CoV-2 nucleocapsid (N) protein is known to manipulate host immunity. Here, we hypothesised that it co-opts the mitochondrial antiviral signalling regulator gC1qR to suppress MAVS dependent interferon responses. To test this, we isolated gC1qR-N complexes by size exclusion chromatography and determined their structures by single particle cryo-EM. Grids were prepared by canonical blotting (Vitrobot) and automated blot free dispensing (Chameleon), and data were processed by RELION and cryoSPARC. Non-uniform refinement yielded mid resolution (~5 Å) maps for the complexes, and 3.8 Å for unbound gC1qR. 3D reconstructions reveal that the trimeric gC1qR ring is engaged by N at its acidic S-face. The N-terminal domain (N-NTD) docks into an acidic pocket on the S-face at the G1 site. This pocket overlaps with the FXII-FnII binding site on gC1qR, suggesting that N could modulate HK-FXII-gC1qR interactions. In addition to the trimer, we observed novel gC1qR tetrameric assemblies bound to N, with an expanded central cavity and an extra protomer in the ring. These tetramers, reported here for the first time, similarly engage N at the S-face through its N-NTD. These structures provide mechanistic insight into how SARS-CoV-2 N hijacks gC1qR to promote immune evasion pathways. By occupying gC1qR’s surface pockets (e.g. those for complement and kinin activation), N may neutralise gC1qR’s proinflammatory functions and disrupt host antiviral pathways. Our findings highlight gC1qR as a viral host cofactor exploited by SARS-CoV-2 to evade the antiviral signalling pathway via N protein interaction. We identify the gC1qR-N interface as a target for host-directed antiviral strategies. This work illustrates how cryo-EM can capture dynamic host-pathogen interfaces and inform the design of interventions targeting co-opted host factors.
Ruiz Campoy Reyes (Thu,) studied this question.