8SUZ

Open State of the SARS-CoV-2 Envelope Protein Transmembrane Domain, Determined by Solid-State NMR


Experimental Data Snapshot

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 3000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Atomic structure of the open SARS-CoV-2 E viroporin.

Medeiros-Silva, J.Dregni, A.J.Somberg, N.H.Duan, P.Hong, M.

(2023) Sci Adv 9: eadi9007-eadi9007

  • DOI: https://doi.org/10.1126/sciadv.adi9007
  • Primary Citation of Related Structures:  
    8SUZ

  • PubMed Abstract: 

    The envelope (E) protein of the SARS-CoV-2 virus forms cation-conducting channels in the endoplasmic reticulum Golgi intermediate compartment (ERGIC) of infected cells. The calcium channel activity of E is associated with the inflammatory responses of COVID-19. Using solid-state NMR (ssNMR) spectroscopy, we have determined the open-state structure of E's transmembrane domain (ETM) in lipid bilayers. Compared to the closed state, open ETM has an expansive water-filled amino-terminal chamber capped by key glutamate and threonine residues, a loose phenylalanine aromatic belt in the middle, and a constricted polar carboxyl-terminal pore filled with an arginine and a threonine residue. This structure gives insights into how protons and calcium ions are selected by ETM and how they permeate across the hydrophobic gate of this viroporin.


  • Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.


Macromolecules
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 
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 3000 
  • 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 Allergy and Infectious Diseases (NIH/NIAID)United StatesGM088204
Netherlands Organisation for Scientific Research (NWO)Netherlands452020132

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references