7QCT | pdb_00007qct

PDZ2 of LNX2 with SARS-CoV-2_E PBM complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.239 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.228 (Depositor) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Interactions of Severe Acute Respiratory Syndrome Coronavirus 2 Protein E With Cell Junctions and Polarity PSD-95/Dlg/ZO-1-Containing Proteins.

Zhu, Y.Alvarez, F.Wolff, N.Mechaly, A.Brule, S.Neitthoffer, B.Etienne-Manneville, S.Haouz, A.Boeda, B.Caillet-Saguy, C.

(2022) Front Microbiol 13: 829094-829094

  • DOI: https://doi.org/10.3389/fmicb.2022.829094
  • Primary Citation Related Structures: 
    7QCR, 7QCS, 7QCT

  • PubMed Abstract: 

    The C-terminus of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protein E contains a PBM (PDZ-binding motif) targeting PDZ (PSD-95/Dlg/ZO-1) domains, which is identical to the PBM of SARS-CoV. The latter is involved in the pathogenicity of the virus. Recently, we identified 10 human PDZ-containing proteins showing significant interactions with SARS-CoV-2 protein E PBM. We selected several of them involved in cellular junctions and cell polarity (TJP1, PARD3, MLLT4, and LNX2) and MPP5/PALS1 previously shown to interact with SARS-CoV E PBM. Targeting cellular junctions and polarity components is a common strategy by viruses to hijack cell machinery to their advantage. In this study, we showed that these host PDZ domains TJP1, PARD3, MLLT4, LNX2, and MPP5/PALS1 interact in a PBM-dependent manner in vitro and colocalize with the full-length E protein in cellulo , sequestrating the PDZ domains to the Golgi compartment. We solved three crystal structures of complexes between human LNX2, MLLT4, and MPP5 PDZs and SARS-CoV-2 E PBM highlighting its binding preferences for several cellular targets. Finally, we showed different affinities for the PDZ domains with the original SARS-CoV-2 C-terminal sequence containing the PBM and the one of the beta variant that contains a mutation close to the PBM. The acquired mutations in the E protein localized near the PBM might have important effects both on the structure and the ion-channel activity of the E protein and on the host machinery targeted by the variants during the infection.


  • Organizational Affiliation
    • Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 23.08 kDa 
  • Atom Count: 1,483 
  • Modeled Residue Count: 190 
  • Deposited Residue Count: 212 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ligand of Numb protein X 2
A, B
94Homo sapiensMutation(s): 0 
Gene Names: LNX2PDZRN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N448 (Homo sapiens)
Explore Q8N448 
Go to UniProtKB:  Q8N448
PHAROS:  Q8N448
GTEx:  ENSG00000139517 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N448
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope small membrane protein
C, D
12Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.239 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.228 (Depositor) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.23α = 90
b = 183.23β = 90
c = 183.23γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Pasteur InstituteFranceURGENCE COVID-19 fundraising campaign
Agence Nationale de la Recherche (ANR)FranceANR Recherche Action Covid19 FRM PDZCov2
Pasteur InstituteFranceDON MICHELIN COVID PFR-5 Cov-2-Cvnet

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description