6XDC

Cryo-EM structure of SARS-CoV-2 ORF3a


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs.

Kern, D.M.Sorum, B.Mali, S.S.Hoel, C.M.Sridharan, S.Remis, J.P.Toso, D.B.Kotecha, A.Bautista, D.M.Brohawn, S.G.

(2021) Nat Struct Mol Biol 28: 573-582

  • DOI: 10.1038/s41594-021-00619-0
  • Primary Citation of Related Structures:  
    6XDC, 7KJR

  • PubMed Abstract: 
  • SARS-CoV-2 ORF3a is a putative viral ion channel implicated in autophagy inhibition, inflammasome activation and apoptosis. 3a protein and anti-3a antibodies are found in infected patient tissues and plasma. Deletion of 3a in SARS-CoV-1 reduces viral titer and morbidity in mice, suggesting it could be an effective target for vaccines or therapeutics ...

    SARS-CoV-2 ORF3a is a putative viral ion channel implicated in autophagy inhibition, inflammasome activation and apoptosis. 3a protein and anti-3a antibodies are found in infected patient tissues and plasma. Deletion of 3a in SARS-CoV-1 reduces viral titer and morbidity in mice, suggesting it could be an effective target for vaccines or therapeutics. Here, we present structures of SARS-CoV-2 3a determined by cryo-EM to 2.1-Å resolution. 3a adopts a new fold with a polar cavity that opens to the cytosol and membrane through separate water- and lipid-filled openings. Hydrophilic grooves along outer helices could form ion-conduction paths. Using electrophysiology and fluorescent ion imaging of 3a-reconstituted liposomes, we observe Ca 2+ -permeable, nonselective cation channel activity, identify mutations that alter ion permeability and discover polycationic inhibitors of 3a activity. 3a-like proteins are found across coronavirus lineages that infect bats and humans, suggesting that 3a-targeted approaches could treat COVID-19 and other coronavirus diseases.


    Related Citations: 
    • Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs.
      Kern, D.M., Sorum, B., Mali, S.S., Hoel, C.M., Sridharan, S., Remis, J.P., Toso, D.B., Kotecha, A., Bautista, D.M., Brohawn, S.G.
      (2021) Biorxiv --: --

    Organizational Affiliation

    California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA. brohawn@berkeley.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ORF3a proteinA, B284Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: 3a
Membrane Entity: Yes 
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM128263
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM123496

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2021-01-27
    Changes: Structure summary
  • Version 1.3: 2021-08-18
    Changes: Database references
  • Version 1.4: 2022-08-31
    Changes: Database references