8HBL | pdb_00008hbl

Crystal structure of the SARS-unique domain (SUD) of SARS-CoV-2 (1.58 angstrom resolution)

• PDB DOI: https://doi.org/10.2210/pdb8HBL/pdb

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


• Deposited: 2022-10-29 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: 1.58 Å
• R-Value Free: 
  0.180 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

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 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.
Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, 100730, Beijing, China.
State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
Department of Microbiology, Li Ka Shing, Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
Swiss Light Source at the Paul Scherrer Institute, 5232, Villigen, Switzerland.
State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. [e-mail].
Department of Microbiology, Li Ka Shing, Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China. [e-mail].
NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology Chinese Academy of Medical Sciences & Peking Union Medical College, 100730, Beijing, China. [e-mail].
Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, 100730, Beijing, China. [e-mail].

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: 29.05 kDa 
• Atom Count: 2,201 
• Modeled Residue Count: 252 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 3	A	260	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
LI (Subject of Investigation/LOI)	C [auth A]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.180 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.671	α = 90
b = 85.671	β = 90
c = 76.662	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	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	81772107

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: 2024-10-30
  Changes: Structure summary