SARS-CoV-2 Envelope Protein Transmembrane Domain: Pentameric Structure Determined by Solid-State NMR

Experimental Data Snapshot

  • Conformers Calculated: 192 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 2.5 of the entry. See complete history


Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers.

Mandala, V.S.McKay, M.J.Shcherbakov, A.A.Dregni, A.J.Kolocouris, A.Hong, M.

(2020) Nat Struct Mol Biol 27: 1202-1208

  • DOI: https://doi.org/10.1038/s41594-020-00536-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    An essential protein of the SARS-CoV-2 virus, the envelope protein E, forms a homopentameric cation channel that is important for virus pathogenicity. Here we report a 2.1-Å structure and the drug-binding site of E's transmembrane domain (ETM), determined using solid-state NMR spectroscopy. In lipid bilayers that mimic the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane, ETM forms a five-helix bundle surrounding a narrow pore. The protein deviates from the ideal α-helical geometry due to three phenylalanine residues, which stack within each helix and between helices. Together with valine and leucine interdigitation, these cause a dehydrated pore compared with the viroporins of influenza viruses and HIV. Hexamethylene amiloride binds the polar amino-terminal lumen, whereas acidic pH affects the carboxy-terminal conformation. Thus, the N- and C-terminal halves of this bipartite channel may interact with other viral and host proteins semi-independently. The structure sets the stage for designing E inhibitors as antiviral drugs.

  • Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope small membrane protein
A, B, C, D, E
31Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: E4
Membrane Entity: Yes 
Find proteins for P0DTC4 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC4 
Go to UniProtKB:  P0DTC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Conformers Calculated: 192 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

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 StatesGM088204

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 2.0: 2020-10-21
    Type: Coordinate replacement
    Reason: Polymer geometry
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2020-10-28
    Changes: Database references
  • Version 2.2: 2020-11-25
    Changes: Database references
  • Version 2.3: 2020-12-16
    Changes: Database references
  • Version 2.4: 2023-06-14
    Changes: Database references, Other
  • Version 2.5: 2024-05-15
    Changes: Data collection, Database references