Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Predict Membrane 

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: 3150 
• Modelled Residue Count: 386 
• Deposited Residue Count: 568 
• Unique protein chains: 1

6XDC

Cryo-EM structure of SARS-CoV-2 ORF3a

• PDB DOI: 10.2210/pdb6XDC/pdb
• EM Map EMD-22136:EMDBEMDataResource

• 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 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 

• PubMed: 32587976 
• DOI: 10.1101/2020.06.17.156554
• Primary Citation of Related Structures:  
  6XDC, 7KJR


• PubMed Abstract: 
  

SARS-CoV-2 encodes three putative ion channels: E, 8a, and 3a. In related SARS-CoV-1, 3a is implicated in viral release, inflammasome activation, and cell death and its deletion reduces viral titer and morbidity in animal models, suggesting 3a-targeted therapeutics could treat SARS and COVID-19. However, the structural basis for the function of 3a is unknown. Here, we show that SARS-CoV-2 forms large conductance cation channels and present cryo-EM structures of dimeric and tetrameric SARS-CoV-2 3a in lipid nanodiscs. 3a adopts a novel fold and is captured in a closed or inactivated state. A narrow bifurcated exterior pore precludes conduction and leads to a large polar cavity open to the cytosol. 3a function is conserved in a common variant among circulating SARS-CoV-2 that alters the channel pore. We identify 3a-like proteins in Alpha- and Beta-coronaviruses that infect bats and humans, suggesting therapeutics targeting 3a could treat a range of coronaviral diseases.

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Organizational Affiliation: 

Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.

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 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-06-10 
• 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