8U1T

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


Experimental Data Snapshot

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 14 
  • 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

Dimeric Transmembrane Structure of the SARS-CoV-2 E Protein.

Zhang, R.Qin, H.Prasad, R.Fu, R.Zhou, H.X.Cross, T.A.

(2023) Commun Biol 6: 1109-1109

  • DOI: https://doi.org/10.1038/s42003-023-05490-x
  • Primary Citation of Related Structures:  
    8U1T

  • PubMed Abstract: 

    The SARS-CoV-2 E protein is a transmembrane (TM) protein with its N-terminus exposed on the external surface of the virus. At debate is its oligomeric state, let alone its function. Here, the TM structure of the E protein is characterized by oriented sample and magic angle spinning solid-state NMR in lipid bilayers and refined by molecular dynamics simulations. This protein was previously found to be a pentamer, with a hydrophobic pore that appears to function as an ion channel. We identify only a front-to-front, symmetric helix-helix interface, leading to a dimeric structure that does not support channel activity. The two helices have a tilt angle of only 6°, resulting in an extended interface dominated by Leu and Val sidechains. While residues Val14-Thr35 are almost all buried in the hydrophobic region of the membrane, Asn15 lines a water-filled pocket that potentially serves as a drug-binding site. The E and other viral proteins may adopt different oligomeric states to help perform multiple functions.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope small membrane protein
A, B
29Severe 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: 100 
  • Conformers Submitted: 14 
  • 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 StatesAI119187
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122698
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118091
National Science Foundation (NSF, United States)United StatesDMR1644779
National Science Foundation (NSF, United States)United StatesDMR2128556

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references