{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T00:29:25Z","timestamp":1787790565067,"version":"build-2784847793"},"reference-count":58,"publisher":"American Society for Microbiology","issue":"5","license":[{"start":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T00:00:00Z","timestamp":1779148800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T00:00:00Z","timestamp":1779148800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2030601"],"award-info":[{"award-number":["2030601"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P41GM111135"],"award-info":[{"award-number":["P41GM111135"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Virol"],"published-print":{"date-parts":[[2026,5,19]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Positive-strand RNA viruses remodel host intracellular membranes to form replication organelles in the cytoplasm. SARS-CoV-2 and other coronaviruses, members of the\n                      <jats:italic toggle=\"yes\">Nidovirales<\/jats:italic>\n                      order, replicate within double-membrane vesicles (DMVs) derived from the endoplasmic reticulum that protect newly synthesized viral RNA (vRNA). A recently discovered SARS-CoV-2 molecular pore complex composed of non-structural proteins 3 and 4 (nsp3 and nsp4) connects the DMV interior with the cytoplasm, enabling vRNA export for subsequent packaging into virions. The C-terminal region of nsp3, the Y domain, oligomerizes to form the base of the cytosolic crown of this pore, while the preceding transmembrane domain 2 (TM2) anchors the pore in the DMV membrane. However, the molecular mechanisms underlying pore formation and whether similar structures are conserved across other\n                      <jats:italic toggle=\"yes\">Nidovirales<\/jats:italic>\n                      members remain unclear. Here, we combined AlphaFold structure prediction, structure-informed multiple sequence alignments, and molecular dynamics simulations to investigate the conservation and potential function of the C-terminal TM2-Y region of nsp3 across nidoviruses. We show that despite minimal sequence identity, all modeled TM2-Y regions adopt similar domain folds. In particular, the wedge-shaped TM2, the Zn-binding Y1 subdomain, and its adjacent Y2 subdomain constitute a conserved structural module present in most vertebrate-infecting\n                      <jats:italic toggle=\"yes\">Nidovirales<\/jats:italic>\n                      families, including\n                      <jats:italic toggle=\"yes\">Coronaviridae<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Tobaniviridae<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Gresnaviridae<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">Olifoviridae,<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">Arteriviridae<\/jats:italic>\n                      . Across these viruses, Zn(II) is coordinated with a distinctive octahedral geometry involving two water molecules. This conserved architecture likely represents an evolutionarily maintained mechanism for DMV pore formation, in which the Zn-binding region engages the membrane surface to induce local lipid bilayer destabilization that may precede DMV pore assembly.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>Over the last 25 years, several coronaviruses, including highly pathogenic SARS-CoV, MERS-CoV, and SARS-CoV-2, have emerged in humans through zoonotic transmission. With nearly 100 coronaviruses known, further spillovers remain possible. Coronaviruses and other nidoviruses replicate within specialized replication organelles formed from host membranes; however, how they form remains poorly understood. This study reveals that coronaviruses and distantly related tobaniviruses and arteriviruses might share a conserved molecular framework for assembling membrane pores that connect the DMV interior, where vRNA is synthetized, and the cytoplasm, where virions are assembled. By identifying conserved structural elements in the C-terminal region of nsp3, including wedge-shaped TM2 domain and Zn-binding Y1\/Y2 tandem, we show that vertebrate-infecting nidoviruses likely share structural mechanism for DMV pore formation. These findings provide insight into how diverse nidoviruses remodel host membranes and highlight the C-terminal region of nsp3 as a potential target for broad-spectrum antivirals.<\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/jvi.02038-25","type":"journal-article","created":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T13:00:19Z","timestamp":1775221219000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":3,"title":["The DMV pore-forming TM2\u2013Y region of SARS-CoV-2 nsp3 exhibits structural conservation beyond the coronavirus family"],"prefix":"10.1128","volume":"100","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8602-1790","authenticated-orcid":true,"given":"Alexandra","family":"Pozhidaeva","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02kzs4y22","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Molecular Biology and 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