9VCK | pdb_00009vck

Cryo-EM structure of SARS-CoV-2 nsp10/nsp14:RNA:SMP complex

• PDB DOI: https://doi.org/10.2210/pdb9VCK/pdb
• EM Map EMD-64956: EMDB EMDataResource
• NAKB: 9VCK

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


• Deposited: 2025-06-06 Released: 2025-07-16 
• Deposition Author(s): Wang, J., Lou, Z., Liu, D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Basis and Rational Design of Nucleotide Analogue Inhibitor Evading the SARS-CoV-2 Proofreading Enzyme.

Wang, J., Pan, Y., Liu, Y., Huang, B., Jin, G., Zhang, L., Zhou, F., Chang, X., Huang, Y., Yan, L., Dong, Y., Rao, Z., Liu, D., Lou, Z.

(2025) J Am Chem Soc 147: 21896-21906

• PubMed: 40509573 
• DOI: https://doi.org/10.1021/jacs.5c05014
• Primary Citation Related Structures: 
  9VCK, 9VCL


• PubMed Abstract: 
  

  All coronaviruses (CoVs) encode an exoribonuclease in nonstructural protein nsp14 (nsp14 ExoN), which is required for the excision of mismatched nucleotides or nucleotide analogues (NAs) that are incorporated into nascent RNA. Here, we investigated the mechanism by which NAs evade SARS-CoV-2 nsp14 ExoN cleavage using chemically synthesized RNA with NAs incorporated at the 3' end. Nsp14 ExoN exhibited significantly attenuated activity on RNA with sofosbuvir monophosphate (SMP) compared with natural nucleotides, remdesivir/molnupiravir monophosphate, and, in particular, AT-9010 monophosphate (ATMP), which has the same chemically modified ribose moiety as SMP, incorporated at the 3' end. Cryo-electron microscopy structures of nsp10/14 bound to RNA-SMP/-ATMP and mutagenesis studies revealed the essential roles of H95/Q145/F146 in recognizing the base moiety and thus pulling the NAs into a favored conformation for cleavage. Therefore, NAs may evade nsp14 ExoN cleavage by having (1) a base that does not interact with H95, Q145, or F146 and (2) a chemically modified ribose. Guided by this hypothesis, two NAs were designed to effectively resist nsp14 ExoN cleavage. These results inform the rational design of anti-CoV NAs.

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Organizational Affiliation: 
• MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, China.
MOE Engineering Research Center of Advanced Rare Earth Materials, Department of Chemistry, Tsinghua University, Beijing 100084, China.
Beijing StoneWise Technology Co Ltd., Beijing 100080, China.
Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
School of Pharmaceutical Sciences, State key laboratory of antiviral drugs, Zhengzhou University, Zhengzhou 450001, China.
State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin 300073, China.
CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
Guangzhou Laboratory, Guangzhou 511442, China.
Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Hum, Kowloon 999077, Hong Kong.
PolyU Shenzhen Research Institute, Shenzhen 518057, China.

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 91.06 kDa 
• Atom Count: 6,213 
• Modeled Residue Count: 697 
• Deposited Residue Count: 707 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 10	A	131	Severe acute respiratory syndrome coronavirus 2	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine-N7 methyltransferase nsp14	B	522	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.1.1.56 (PDB Primary Data), 3.1.13 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (26-MER)	C [auth P]	26	Severe acute respiratory syndrome coronavirus 2

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (28-MER)	D [auth T]	28	Severe acute respiratory syndrome coronavirus 2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K5X (Subject of Investigation/LOI)	L [auth P]	[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate C10 H14 F N2 O8 P JAJZLQMRDFLNSW-VPCXQMTMSA-N
ZN	E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.22 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.16_3549
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Wang, J., Lou, Z., Liu, D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32188101
National Natural Science Foundation of China (NSFC)	China	22477122

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release