7NTK | pdb_00007ntk

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

• PDB DOI: https://doi.org/10.2210/pdb7NTK/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-03-10 Released: 2021-06-16 
• Deposition Author(s): Javorsky, A., Kvansakul, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 34117354 
• DOI: https://doi.org/10.1038/s42003-021-02250-7
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Vic, Australia.
Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Vic, Australia. [e-mail].
Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Vic, Australia. [e-mail].
Department of Biochemistry & Molecular Biology, University of Melbourne, Melbourne, Vic, Australia. [e-mail].
Department of Clinical Pathology, University of Melbourne, Melbourne, Vic, Australia. [e-mail].
Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Vic, Australia. [e-mail].
Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Vic, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.66 kDa 
• Atom Count: 3,155 
• Modeled Residue Count: 370 
• Deposited Residue Count: 380 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAGUK p55 subfamily member 5	A, B, D, F	87	Homo sapiens	Mutation(s): 0  Gene Names: MPP5, PALS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N3R9 (Homo sapiens) Explore Q8N3R9  Go to UniProtKB:  Q8N3R9
PHAROS:  Q8N3R9 GTEx:  ENSG00000072415

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope small membrane protein	C, E, G, H	8	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC4 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC4  Go to UniProtKB:  P0DTC4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	I [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
EDO	J [auth B], K [auth B], L [auth B], M [auth D], N [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.688	α = 90
b = 103.762	β = 103.979
c = 59.076	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-16 
Deposition Author(s): Javorsky, A., Kvansakul, M.

Revision History  

• 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