Structure of SARS-CoV-2 Orf3a in plasma membrane-like environment, MSP1D1 nanodisc

Experimental Data Snapshot

  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins.

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.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.84477
  • Primary Citation of Related Structures:  
    8EQJ, 8EQS, 8EQT, 8EQU

  • 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.

  • Organizational Affiliation

    Janelia Research Campus, Ashburn, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF3a protein
A, B
331Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: 3a
Membrane Entity: Yes 
Find proteins for P0DTC3 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC3 
Go to UniProtKB:  P0DTC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection