7YE8

Crystal structure of SARS-CoV-2 refolded dimeric ORF9b

Summary for 7YE8

• Entry DOI: 10.2210/pdb7ye8/pdb
• Descriptor: ORF9b protein, N-OCTANE (2 entities in total)
• Functional Keywords: sars-cov-2, orf9b, immune escape, viral antagonist, membrane association, fold switch, lipid binding, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV,SARS-CoV-2)
• Total number of polymer chains: 4
• Total formula weight: 46778.53

Authors

Jin, X.,Chai, Y.,Qi, J.,Song, H.,Gao, G.F. (deposition date: 2022-07-05, release date: 2022-10-19, Last modification date: 2023-11-29)

Primary citation

Jin, X.,Sun, X.,Chai, Y.,Bai, Y.,Li, Y.,Hao, T.,Qi, J.,Song, H.,Wong, C.C.L.,Gao, G.F.
Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism.
Sci China Life Sci, 66:152-164, 2023

PubMed Abstract: The constant emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants indicates the evolution and adaptation of the virus. Enhanced innate immune evasion through increased expression of viral antagonist proteins, including ORF9b, contributes to the improved transmission of the Alpha variant; hence, more attention should be paid to these viral proteins. ORF9b is an accessory protein that suppresses innate immunity via a monomer conformation by binding to Tom70. Here, we solved the dimeric structure of SARS-CoV-2 ORF9b with a long hydrophobic tunnel containing a lipid molecule that is crucial for the dimeric conformation and determined the specific lipid ligands as monoglycerides by conducting a liquid chromatography with tandem mass spectrometry analysis, suggesting an important role in the viral life cycle. Notably, a long intertwined loop accessible for host factor binding was observed in the structure. Eight phosphorylated residues in ORF9b were identified, and residues S50 and S53 were found to contribute to the stabilization of dimeric ORF9b. Additionally, we proposed a model of multifunctional ORF9b with a distinct conformation, suggesting that ORF9b is a fold-switching protein, while both lipids and phosphorylation contribute to the switching. Specifically, the ORF9b monomer interacts with Tom70 to suppress the innate immune response, whereas the ORF9b dimer binds to the membrane involving mature virion assembly. Our results provide a better understanding of the multiple functions of ORF9b.

PubMed: 36184694
DOI: 10.1007/s11427-022-2168-8

Experimental method

X-RAY DIFFRACTION (3.01 Å)