8XKO | pdb_00008xko

CryoEM structure of compound HNC-1664 bound with RdRP-RNA complex of SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb8XKO/pdb
• NAKB: 8XKO
• EM Map EMD-38422: EMDB EMDataResource

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Severe acute respiratory syndrome coronavirus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-23 Released: 2024-12-04 
• Deposition Author(s): Li, M., An, L., Hong, Y., Li, S., Zhang, K.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

An adenosine analog shows high antiviral potency against coronavirus and arenavirus mainly through an unusual base pairing mode.

Jia, X., Jing, X., Li, M., Gao, M., Zhong, Y., Li, E., Liu, Y., Li, R., Yao, G., Liu, Q., Zhou, M., Hou, Y., An, L., Hong, Y., Li, S., Zhang, J., Wang, W., Zhang, K., Gong, P., Chiu, S.

(2024) Nat Commun 15: 10750-10750

• PubMed: 39737930 
• DOI: https://doi.org/10.1038/s41467-024-54918-3
• Primary Citation Related Structures: 
  8XKO, 8XPO, 8XPP


• PubMed Abstract: 
  

  By targeting the essential viral RNA-dependent RNA polymerase (RdRP), nucleoside analogs (NAs) have exhibited great potential in antiviral therapy for RNA virus-related diseases. However, most ribose-modified NAs do not present broad-spectrum features, likely due to differences in ribose-RdRP interactions across virus families. Here, we show that HNC-1664, an adenosine analog with modifications both in ribose and base, has broad-spectrum antiviral activity against positive-strand coronaviruses and negative-strand arenaviruses. Importantly, treatment with HNC-1664 demonstrate anti-SARS-CoV-2 efficacy in infected K18-human ACE2 mice, with reduced viral titer and mortality, as well as improved lung injury. Enzymology data demonstrate that HNC-1664 inhibits RNA synthesis mainly at the pre-catalysis stage. The cryo-EM structures of HNC-1664-bound RdRP-RNA complexes from both SARS-CoV-2 and LASV reveal an unusual base pairing mode of HNC-1664 in part due to its base modification, thus revealing its great potency in binding but not catalysis. Under certain circumstances, 1664-TP can be slowly incorporated by RdRP through regular Watson-Crick base pairing, as evidenced by enzymology data and an HNC-1664-incorporated crystal structure of the RdRP-RNA complex. Overall, HNC-1664 achieves broad-spectrum characteristics by favoring an alternative base pairing strategy to non-catalytically block RNA synthesis, providing a novel concept for the rational development of NA drugs.

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Organizational Affiliation: 
• Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei, China.
Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
University of Chinese Academy of Sciences, Beijing, China.
Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China. [e-mail].
Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei, China. [e-mail].
Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China. [e-mail].
MOE Key Laboratory for Cellular Dynamics and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Hefei, China. [e-mail].
Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, Anhui, China. [e-mail].
Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei, China. [e-mail].
Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, China. [e-mail].
Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China. [e-mail].
Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China. [e-mail].
Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, Anhui, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 176.5 kDa 
• Atom Count: 10,647 
• Modeled Residue Count: 1,281 
• Deposited Residue Count: 1,486 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase nsp12	A	944	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.7.7.48 (PDB Primary Data), 2.7.7.50 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	B, D	210	Severe acute respiratory syndrome coronavirus	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	C	89	Severe acute respiratory syndrome coronavirus	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*UP*AP*CP*GP*CP*GP*UP*AP*GP*CP*AP*UP*G)-3')	E	14	synthetic construct

Entity ID: 5
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*UP*CP*AP*UP*GP*CP*UP*AP*CP*GP*CP*GP*UP*AP*G)-3')	F	19	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1LVZ	G [auth A]	[[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-(5-iodanyl-4-methyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate C12 H16 F I N3 O12 P3 SDPCZQPAUGWGIT-DLYFRVTGSA-N
MG	H [auth A], I [auth A], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Li, M., An, L., Hong, Y., Li, S., Zhang, K.

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Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release
  
• Version 1.1: 2025-01-15
  Changes: Data collection, Database references
• Version 1.2: 2025-07-02
  Changes: Data collection