Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs

Abstract

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes the coronavirus disease 2019 (COVID-19). SARS-CoV-2 encodes three putative ion channels: E, 8a, and 3a 1,2 . 3a is expressed in SARS patient tissue and anti-3a antibodies are observed in patient plasma 3–6 . 3a has been implicated in viral release 7 , inhibition of autophagy 8 , inflammasome activation 9 , and cell death 10,11 and its deletion reduces viral titer and morbidity in mice 1 , raising the possibility that 3a could be an effective vaccine or therapeutic target 3,12 . Here, we present the first cryo-EM structures of SARS-CoV-2 3a to 2.1 Å resolution and demonstrate 3a forms an ion channel in reconstituted liposomes. The structures in lipid nanodiscs reveal 3a dimers and tetramers adopt a novel fold with a large polar cavity that spans halfway across the membrane and is accessible to the cytosol and the surrounding bilayer through separate water- and lipid-filled openings. Electrophysiology and fluorescent ion imaging experiments show 3a forms Ca 2+ -permeable non-selective cation channels. We identify point mutations that alter ion permeability and discover polycationic inhibitors of 3a channel activity. We find 3a-like proteins in multiple Alphacoronavirus and Betacoronavirus lineages that infect bats and humans. These data show 3a forms a functional ion channel that may promote COVID-19 pathogenesis and suggest targeting 3a could broadly treat coronavirus diseases.