9Q1J | pdb_00009q1j

Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 E191A mutant-T20P14-R complex

• PDB DOI: https://doi.org/10.2210/pdb9Q1J/pdb
• EM Map EMD-72127: EMDB EMDataResource
• NAKB: 9Q1J

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


• Deposited: 2025-08-14 Released: 2025-09-24 
• Deposition Author(s): Yang, Y., Liu, C., Liu, B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.81 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Molecular basis of SARS-CoV-2 proofreading enzyme-mediated resistance to remdesivir.

Yang, Y., Li, Y., Becker, S.T., Khan, A., Luo, G., Liu, B., Liu, C.

(2025) Proc Natl Acad Sci U S A 122: e2519755122-e2519755122

• PubMed: 41032524 
• DOI: https://doi.org/10.1073/pnas.2519755122
• Primary Citation of Related Structures:  
  9Q1J


• PubMed Abstract: 
  

  SARS-CoV-2's remarkable resistance to nucleotide analog antivirals such as remdesivir, which thwarts RNA synthesis by inhibiting viral polymerase (RdRp), challenges available therapies. We reveal that remdesivir incorporation destabilizes RdRp-RNA complex while enhancing RNA binding to the proofreading exoribonuclease (ExoN), facilitating remdesivir excision. Conserved ExoN determinants for remdesivir recognition and excision underpin ExoN-mediated resistance across all coronaviruses. These findings inform the design of next-generation antivirals and combination therapies capable of overcoming ExoN-mediated resistance.

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Organizational Affiliation: 
• Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011.
Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205.
Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 329.25 kDa 
• Atom Count: 21,410 
• Modeled Residue Count: 2,630 
• Deposited Residue Count: 2,756 
• 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, C, G, I	139	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
Proofreading exoribonuclease	B, D, H, J	527	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 3.1.13
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
T20P14-R RNA	E, K	39	Severe acute respiratory syndrome coronavirus 2

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*A*UP*UP*CP*CP*CP*C)-3')	F, L	7	Severe acute respiratory syndrome coronavirus 2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	BA [auth H], CA [auth H], DA [auth H], EA [auth I], FA [auth I], HA [auth J], IA [auth J], JA [auth J], M [auth A], N [auth A], P [auth B], Q [auth B], R [auth B], S [auth C], T [auth C], V [auth D], W [auth D], X [auth D], Y [auth G], Z [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AA [auth H], GA [auth J], O [auth B], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.81 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Yang, Y., Liu, C., Liu, B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM150607
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	DP2AI177906

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release
  
• Version 1.1: 2025-10-15
  Changes: Data collection, Database references