8EQS

Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like environment, MSP1D1 nanodisc

Summary for 8EQS

• Entry DOI: 10.2210/pdb8eqs/pdb
• EMDB information: 28544
• Descriptor: ORF3a protein, Apolipoprotein A-I, 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (3 entities in total)
• Functional Keywords: membrane protein, sars-cov, sars-cov-2, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus (SARS-CoV); More
• Total number of polymer chains: 4
• Total formula weight: 123433.96

Authors

Miller, A.N.,Houlihan, P.R.,Matamala, E.,Cabezas-Bratesco, D.,Lee, G.Y.,Cristofori-Armstrong, B.,Dilan, T.L.,Sanchez-Martinez, S.,Matthies, D.,Yan, R.,Yu, Z.,Ren, D.,Brauchi, S.E.,Clapham, D.E. (deposition date: 2022-10-09, release date: 2023-02-08, Last modification date: 2024-06-19)

Primary citation

Miller, A.N.,Houlihan, P.R.,Matamala, E.,Cabezas-Bratesco, D.,Lee, G.Y.,Cristofori-Armstrong, B.,Dilan, T.L.,Sanchez-Martinez, S.,Matthies, D.,Yan, R.,Yu, Z.,Ren, D.,Brauchi, S.E.,Clapham, D.E.
The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins.
Elife, 12:-, 2023

PubMed Abstract: The severe acute respiratory syndrome associated coronavirus 2 (SARS-CoV-2) and SARS-CoV-1 accessory protein Orf3a colocalizes with markers of the plasma membrane, endocytic pathway, and Golgi apparatus. Some reports have led to annotation of both Orf3a proteins as viroporins. Here, we show that neither SARS-CoV-2 nor SARS-CoV-1 Orf3a form functional ion conducting pores and that the conductances measured are common contaminants in overexpression and with high levels of protein in reconstitution studies. Cryo-EM structures of both SARS-CoV-2 and SARS-CoV-1 Orf3a display a narrow constriction and the presence of a positively charged aqueous vestibule, which would not favor cation permeation. We observe enrichment of the late endosomal marker Rab7 upon SARS-CoV-2 Orf3a overexpression, and co-immunoprecipitation with VPS39. Interestingly, SARS-CoV-1 Orf3a does not cause the same cellular phenotype as SARS-CoV-2 Orf3a and does not interact with VPS39. To explain this difference, we find that a divergent, unstructured loop of SARS-CoV-2 Orf3a facilitates its binding with VPS39, a HOPS complex tethering protein involved in late endosome and autophagosome fusion with lysosomes. We suggest that the added loop enhances SARS-CoV-2 Orf3a's ability to co-opt host cellular trafficking mechanisms for viral exit or host immune evasion.

PubMed: 36695574
DOI: 10.7554/eLife.84477

Experimental method

ELECTRON MICROSCOPY (3.1 Å)