Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 64.33 kDa 
• Atom Count: 3,150 
• Modelled Residue Count: 386 
• Deposited Residue Count: 568 
• Unique protein chains: 1

 6XDC

Cryo-EM structure of SARS-CoV-2 ORF3a

• PDB DOI:  https://doi.org/10.2210/pdb6XDC/pdb
• EM Map EMD-22136: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMMemProtMD


• Deposited: 2020-06-10 Released: 2020-06-17 
• Deposition Author(s): Kern, D.M., Hoel, C.M., Brohawn, S.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

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

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

• PubMed: 34158638 
• DOI: https://doi.org/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. 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.

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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 --: --

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Organizational Affiliation: 

California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF3a protein	A, B	284	Severe acute respiratory syndrome coronavirus 2	Mutation(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

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2
MODEL REFINEMENT	PHENIX	1.17.1-3660

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Kern, D.M., Hoel, C.M., Brohawn, S.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM128263
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM123496

Revision History  

• 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