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

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 3a1,2. 3a is expressed in SARS patient tissue and anti-3a antibodies are observed in patient plasma3–6. 3...

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Bibliographic Details
Published in:bioRxiv 2021-01
Main Authors: Kern, David M, Sorum, Ben, Mali, Sonali S, Hoel, Christopher M, Sridharan, Savitha, Remis, Jonathan P, Toso, Daniel B, Kotecha, Abhay, Bautista, Diana M, Brohawn, Stephen G
Format: Article
Language:English
Subjects:
Animal models
Cell activation
Cell death
Clonal deletion
Conductance
Conduction
Coronaviridae
Coronaviruses
COVID-19
Cytosol
Inflammasomes
Ion channels
Morbidity
Severe acute respiratory syndrome coronavirus 2
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Summary: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 3a1,2. 3a is expressed in SARS patient tissue and anti-3a antibodies are observed in patient plasma3–6. 3a has been implicated in viral release7, inhibition of autophagy8, inflammasome activation9, and cell death10,11 and its deletion reduces viral titer and morbidity in mice1, raising the possibility that 3a could be an effective vaccine or therapeutic target3,12. 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 Ca2+-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. Competing Interest Statement AK is an employee of Thermo Fisher Scientific. Footnotes * https://www.rcsb.org/structure/6XDC * https://www.emdataresource.org/EMD-22136 * https://www.emdataresource.org/EMD-22138 * https://www.emdataresource.org/EMD-22139 * https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10439/ * https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10440/ * https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10441/ * https://www.rcsb.org/structure/7kjr * https://www.emdataresource.org/EMD-22898 * https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10612/
DOI:10.1101/2020.06.17.156554