6LXT

Structure of post fusion core of 2019-nCoV S2 subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion.

Xia, S.Liu, M.Wang, C.Xu, W.Lan, Q.Feng, S.Qi, F.Bao, L.Du, L.Liu, S.Qin, C.Sun, F.Shi, Z.Zhu, Y.Jiang, S.Lu, L.

(2020) Cell Res 30: 343-355

  • DOI: 10.1038/s41422-020-0305-x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The recent outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 infection in Wuhan, China has posed a serious threat to global public health. To develop specific anti-coronavirus therapeutics and prophylactics, the molecular mechanism that ...

    The recent outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 infection in Wuhan, China has posed a serious threat to global public health. To develop specific anti-coronavirus therapeutics and prophylactics, the molecular mechanism that underlies viral infection must first be defined. Therefore, we herein established a SARS-CoV-2 spike (S) protein-mediated cell-cell fusion assay and found that SARS-CoV-2 showed a superior plasma membrane fusion capacity compared to that of SARS-CoV. We solved the X-ray crystal structure of six-helical bundle (6-HB) core of the HR1 and HR2 domains in the SARS-CoV-2 S protein S2 subunit, revealing that several mutated amino acid residues in the HR1 domain may be associated with enhanced interactions with the HR2 domain. We previously developed a pan-coronavirus fusion inhibitor, EK1, which targeted the HR1 domain and could inhibit infection by divergent human coronaviruses tested, including SARS-CoV and MERS-CoV. Here we generated a series of lipopeptides derived from EK1 and found that EK1C4 was the most potent fusion inhibitor against SARS-CoV-2 S protein-mediated membrane fusion and pseudovirus infection with IC50s of 1.3 and 15.8 nM, about 241- and 149-fold more potent than the original EK1 peptide, respectively. EK1C4 was also highly effective against membrane fusion and infection of other human coronavirus pseudoviruses tested, including SARS-CoV and MERS-CoV, as well as SARSr-CoVs, and potently inhibited the replication of 5 live human coronaviruses examined, including SARS-CoV-2. Intranasal application of EK1C4 before or after challenge with HCoV-OC43 protected mice from infection, suggesting that EK1C4 could be used for prevention and treatment of infection by the currently circulating SARS-CoV-2 and other emerging SARSr-CoVs.


    Organizational Affiliation

    Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan-Jinbo Joint Research Center, Fudan University, Shanghai, 200032, China. lul@fudan.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spike protein S2, Spike protein S2
A, B, C, D, E, F
132Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Go to UniProtKB:  P0DTC2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.259 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.24α = 90
b = 57.58β = 91.58
c = 115.72γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2020-02-11 
  • Released Date: 2020-02-26 
  • Deposition Author(s): Zhu, Y., Sun, F.

Revision History 

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2020-04-15
    Changes: Database references
  • Version 1.3: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary