The crystal structure of the SARS-CoV-2 ORF7a ectodomain

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14 + monocytes.

Zhou, Z.Huang, C.Zhou, Z.Huang, Z.Su, L.Kang, S.Chen, X.Chen, Q.He, S.Rong, X.Xiao, F.Chen, J.Chen, S.

(2021) iScience 24: 102187-102187

  • DOI: https://doi.org/10.1016/j.isci.2021.102187
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Dysregulated immune cell responses have been linked to the severity of coronavirus disease 2019 (COVID-19), but the specific viral factors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were currently unknown. Herein, we reveal that the Immunoglobulin-like fold ectodomain of the viral protein SARS-CoV-2 ORF7a interacts with high efficiency to CD14 + monocytes in human peripheral blood, compared to pathogenic protein SARS-CoV ORF7a. The crystal structure of SARS-CoV-2 ORF7a at 2.2 Å resolution reveals three remarkable changes on the amphipathic side of the four-stranded β-sheet, implying a potential functional interface of the viral protein. Importantly, SARS-CoV-2 ORF7a coincubation with CD14 + monocytes ex vivo triggered a decrease in HLA-DR/DP/DQ expression levels and upregulated significant production of proinflammatory cytokines, including IL-6, IL-1β, IL-8, and TNF-α. Our work demonstrates that SARS-CoV-2 ORF7a is an immunomodulating factor for immune cell binding and triggers dramatic inflammatory responses, providing promising therapeutic drug targets for pandemic COVID-19.

  • Organizational Affiliation

    Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orf7a protein84Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: ORF7aNS7aorf7a
Find proteins for P0DTC7 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC7 
Go to UniProtKB:  P0DTC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.545α = 90
b = 37.545β = 90
c = 56.16γ = 120
Software Package:
Software NamePurpose
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770801

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references
  • Version 1.2: 2021-03-17
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description