PALS1 PDZ1 domain with SARS-CoV-2_E PBM complex

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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This is version 1.2 of the entry. See complete history


Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain.

Javorsky, A.Humbert, P.O.Kvansakul, M.

(2021) Commun Biol 4: 724-724

  • DOI: https://doi.org/10.1038/s42003-021-02250-7
  • Primary Citation of Related Structures:  
    7NTJ, 7NTK

  • PubMed Abstract: 

    SARS-CoV-2 infection leads to coronavirus disease 2019 (COVID-19), which is associated with severe and life-threatening pneumonia and respiratory failure. However, the molecular basis of these symptoms remains unclear. SARS-CoV-1 E protein interferes with control of cell polarity and cell-cell junction integrity in human epithelial cells by binding to the PALS1 PDZ domain, a key component of the Crumbs polarity complex. We show that C-terminal PDZ binding motifs of SARS-CoV-1 and SARS-CoV-2 E proteins bind the PALS1 PDZ domain with 29.6 and 22.8 μM affinity, whereas the related sequence from MERS-CoV did not bind. We then determined crystal structures of PALS1 PDZ domain bound to both SARS-CoV-1 and SARS-CoV-2 E protein PDZ binding motifs. Our findings establish the structural basis for SARS-CoV-1/2 mediated subversion of Crumbs polarity signalling and serve as a platform for the development of small molecule inhibitors to suppress SARS-CoV-1/2 mediated disruption of polarity signalling in epithelial cells.

  • Organizational Affiliation

    Department of Biochemistry & Molecular Biology, University of Melbourne, Melbourne, Vic, Australia. p.humbert@latrobe.edu.au.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAGUK p55 subfamily member 5
A, B, D, F
87Homo sapiensMutation(s): 0 
Gene Names: MPP5PALS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N3R9 (Homo sapiens)
Explore Q8N3R9 
Go to UniProtKB:  Q8N3R9
GTEx:  ENSG00000072415 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N3R9
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope small membrane protein
C, E, G, H
8Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Find proteins for P0DTC4 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC4 
Go to UniProtKB:  P0DTC4
Entity Groups  
UniProt GroupP0DTC4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.688α = 90
b = 103.762β = 103.979
c = 59.076γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description