9HM2 | pdb_00009hm2

A swapped dimeric form of ZO1/TJP1 PDZ2 in complex with the C-terminal peptide from protein E of SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb9HM2/pdb

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


• Deposited: 2024-12-06 Released: 2025-10-22 
• Deposition Author(s): Alvarez, F., Mechaly, A., Haouz, A., Caillet-Saguy, C.
• Funding Organization(s): Pasteur Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

HTRF-based identification of small molecules targeting SARS-CoV-2 E protein interaction with ZO-1 PDZ2

Alvarez, F., Larrous, F., Mechaly, A., Bardiaux, B., Goor, Q., Haouz, A., Seon-Meniel, B., De Sousa, R.A., Bourg, S., Figadere, B., Wolff, N., Munier-Lehmann, H., Caillet-Saguy, C.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.07.16.665136

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.99 kDa 
• Atom Count: 1,492 
• Modeled Residue Count: 183 
• Deposited Residue Count: 192 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tight junction protein ZO-1	A, B	84	Homo sapiens	Mutation(s): 0  Gene Names: TJP1, ZO1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07157 (Homo sapiens) Explore Q07157  Go to UniProtKB:  Q07157
PHAROS:  Q07157 GTEx:  ENSG00000104067

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope small membrane protein	C, D	12	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: E, 4
UniProt
Find proteins for P0DTC4 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC4  Go to UniProtKB:  P0DTC4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	E [auth A], F [auth A], G [auth B], H [auth B], I [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.127	α = 90
b = 76.157	β = 90
c = 76.922	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Alvarez, F., Mechaly, A., Haouz, A., Caillet-Saguy, C.

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Funding Organization	Location	Grant Number
Pasteur Institute	France	DON MICHELIN COVID PFR-5 Cov-2-Cvnet

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release