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 2.0 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: 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.


  • Organizational Affiliation

    Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, CA, USA. dbautista@berkeley.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF3a protein
A, B
284Severe 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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein A-I
C, D
210Homo 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
GTEx:  ENSG00000118137 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02647
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / 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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2-3874-000

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
  • Version 2.0: 2022-08-31
    Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary