Molecular architecture of coronavirus double-membrane vesicle pore complex

• Published in: Nature (London) Vol. 633; no. 8028; pp. 224 - 231
• Main Authors: Huang, Yixin, Wang, Tongyun, Zhong, Lijie, Zhang, Wenxin, Zhang, Yu, Yu, Xiulian, Yuan, Shuofeng, Ni, Tao
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 05-09-2024; Nature Publishing Group
• Subjects: 101/28; 101/58; 631/326/596/4130; 631/535/1258/1260; 82/80; 82/83; 96/31; Chemical synthesis; Complex formation; Coronaviruses; COVID-19; Cryoelectron Microscopy; Cryoforming; Electron Microscope Tomography; Genomes; Humanities and Social Sciences; Humans; Membranes; Models, Molecular; Molecular structure; multidisciplinary; Nuclear Pore - chemistry; Nuclear Pore - metabolism; Nuclear Pore - ultrastructure; Nuclear pores; Pore formation; Protein Domains; Proteins; Replication; RNA polymerase; RNA viruses; RNA, Viral - chemistry; RNA, Viral - metabolism; SARS-CoV-2 - chemistry; SARS-CoV-2 - genetics; SARS-CoV-2 - metabolism; SARS-CoV-2 - physiology; SARS-CoV-2 - ultrastructure; Science; Science (multidisciplinary); Severe acute respiratory syndrome coronavirus 2; Stoichiometry; Symmetry; Tomography; Topology; Transcription; Translocation; Transmembrane domains; Viral diseases; Viral Nonstructural Proteins - chemistry; Viral Nonstructural Proteins - metabolism; Viral Nonstructural Proteins - ultrastructure; Virus Replication; Viruses
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/s41586-024-07817-y

Coronaviruses remodel the intracellular host membranes during replication, forming double-membrane vesicles (DMVs) to accommodate viral RNA synthesis and modifications
1
,
2
. SARS-CoV-2 non-structural protein 3 (nsp3) and nsp4 are the minimal viral components required to induce DMV formation and to form a double-membrane-spanning pore, essential for the transport of newly synthesized viral RNAs
3
–
5
. The mechanism of DMV pore complex formation remains unknown. Here we describe the molecular architecture of the SARS-CoV-2 nsp3–nsp4 pore complex, as resolved by cryogenic electron tomography and subtomogram averaging in isolated DMVs. The structures uncover an unexpected stoichiometry and topology of the nsp3–nsp4 pore complex comprising 12 copies each of nsp3 and nsp4, organized in 4 concentric stacking hexamer rings, mimicking a miniature nuclear pore complex. The transmembrane domains are interdigitated to create a high local curvature at the double-membrane junction, coupling double-membrane reorganization with pore formation. The ectodomains form extensive contacts in a pseudo-12-fold symmetry, belting the pore complex from the intermembrane space. A central positively charged ring of arginine residues coordinates the putative RNA translocation, essential for virus replication. Our work establishes a framework for understanding DMV pore formation and RNA translocation, providing a structural basis for the development of new antiviral strategies to combat coronavirus infection.
A study details the molecular architecture of the double-membrane-spanning pore formed by the proteins nsp3 and nsp4 in double-membrane vesicles of SARS-CoV-2.