8SUZ | pdb_00008suz

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

• PDB DOI: https://doi.org/10.2210/pdb8SUZ/pdb
• BMRB: 31085

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2023-05-14 Released: 2023-10-25 
• Deposition Author(s): Medeiros-Silva, J., Dregni, A.J., Somberg, N.H., Hong, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

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

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

• PubMed: 37831764 
• DOI: https://doi.org/10.1126/sciadv.adi9007
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis, NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 16.81 kDa 
• Atom Count: 1,190 
• Modeled Residue Count: 155 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope small membrane protein	A, B, C, D, E	31	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: E, 4 Membrane Entity: Yes
UniProt
Find proteins for P0DTC4 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC4  Go to UniProtKB:  P0DTC4

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): Medeiros-Silva, J., Dregni, A.J., Somberg, N.H., Hong, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	GM088204
Netherlands Organisation for Scientific Research (NWO)	Netherlands	452020132

Revision History  

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