Crystal structure of SARS-CoV-2 soluble dimeric ORF9b

Experimental Data Snapshot

  • Resolution: 2.95 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.269 

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Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism.

Jin, X.Sun, X.Chai, Y.Bai, Y.Li, Y.Hao, T.Qi, J.Song, H.Wong, C.C.L.Gao, G.F.

(2023) Sci China Life Sci 66: 152-164

  • DOI: https://doi.org/10.1007/s11427-022-2168-8
  • Primary Citation of Related Structures:  
    7YE7, 7YE8

  • 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.

  • Organizational Affiliation

    School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF9b proteinA [auth C],
B [auth D],
C [auth A],
D [auth B]
103Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: 9b
Find proteins for P0DTD2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD2 
Go to UniProtKB:  P0DTD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.95 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.269 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.579α = 90
b = 73.579β = 90
c = 175.616γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not fundedChina--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2023-01-25
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description