7KJR

Cryo-EM structure of SARS-CoV-2 ORF3a


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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 

  • 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 ...

    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.


    Organizational Affiliation

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



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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Apolipoprotein A-IC, D210Homo sapiensMutation(s): 0 
Gene Names: APOA1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P02647 (Homo sapiens)
Explore P02647 
Go to UniProtKB:  P02647
PHAROS:  P02647
GTEx:  ENSG00000118137 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02647
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEE
Query on PEE

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.08 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 StatesGM123496
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM128263

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Structure summary
  • Version 1.2: 2021-08-18
    Changes: Database references