8GQC

Crystal structure of the SARS-unique domain (SUD) of SARS-CoV-2 (1.35 angstrom resolution)

• PDB DOI: https://doi.org/10.2210/pdb8GQC/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-08-30 Released: 2023-07-12 
• Deposition Author(s): Qin, B., Li, Z., Aumonier, S., Wang, M., Cui, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.162 
• R-Value Work: 0.140 
• R-Value Observed: 0.141 

Starting Model: experimental

Literature

Identification of the SARS-unique domain of SARS-CoV-2 as an antiviral target.

Qin, B., Li, Z., Tang, K., Wang, T., Xie, Y., Aumonier, S., Wang, M., Yuan, S., Cui, S.

(2023) Nat Commun 14: 3999-3999

• PubMed: 37414753 
• DOI: https://doi.org/10.1038/s41467-023-39709-6
• Primary Citation of Related Structures:  
  8GQC, 8HBL


• PubMed Abstract: 
  

  SARS-CoV-2 nsp3 is essential for viral replication and host responses. The SARS-unique domain (SUD) of nsp3 exerts its function through binding to viral and host proteins and RNAs. Herein, we show that SARS-CoV-2 SUD is highly flexible in solution. The intramolecular disulfide bond of SARS-CoV SUD is absent in SARS-CoV-2 SUD. Incorporating this bond in SARS-CoV-2 SUD allowed crystal structure determination to 1.35 Å resolution. However, introducing this bond in SARS-CoV-2 genome was lethal for the virus. Using biolayer interferometry, we screened compounds directly binding to SARS-CoV-2 SUD and identified theaflavin 3,3'-digallate (TF3) as a potent binder, K _d 2.8 µM. TF3 disrupted the SUD-guanine quadruplex interactions and exhibited anti-SARS-CoV-2 activity in Vero E6-TMPRSS2 cells with an EC ₅₀ of 5.9 µM and CC ₅₀ of 98.5 µM. In this work, we provide evidence that SARS-CoV-2 SUD harbors druggable sites for antiviral development.

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Organizational Affiliation: 

NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, Beijing, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.02 kDa 
• Atom Count: 2,247 
• Modelled Residue Count: 246 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	264	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2  EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.162 
• R-Value Work: 0.140 
• R-Value Observed: 0.141 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.012	α = 90
b = 87.012	β = 90
c = 76.774	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
STARANISO	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Qin, B., Li, Z., Aumonier, S., Wang, M., Cui, S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81772207

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-02-14
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Structure summary