9M48 | pdb_00009m48

Cryo-EM structure of 6:1 nsp15/dsRNA complex

• PDB DOI: https://doi.org/10.2210/pdb9M48/pdb
• NAKB: 9M48
• EM Map EMD-63618: EMDB EMDataResource

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


• Deposited: 2025-03-04 Released: 2026-02-11 
• Deposition Author(s): Wang, L., Li, J., Zhu, B., Wang, X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Metal ions govern coronavirus endoribonuclease activity.

Wang, X., Li, J., Liu, Z., Wang, L., Zhu, B.

(2026) Nucleic Acids Res 54

• PubMed: 41533565 
• DOI: https://doi.org/10.1093/nar/gkaf1508
• Primary Citation Related Structures: 
  9M48, 9M49


• PubMed Abstract: 
  

  Coronavirus nonstructural protein 15 (nsp15) is an endoribonuclease that restricts viral double-stranded RNA (dsRNA) accumulation in the cytosol to evade host immunity. Given the co-localization of nsp15 and replicating viral RNA, the mechanism controlling nsp15 activity is essential, yet poorly understood. Although metal ions are widely used as cofactors for enzymes, their role in nsp15 remains elusive. Here, we show that Co2+ or Ni2+ potently activates, whereas Zn2+ inhibits nsp15 of multiple coronaviruses. In the presence of Co2+, cryo-electron microscopy structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nsp15/dsRNA complexes indicate higher dsRNA-binding affinity. Active-site mutation H249A weakens the effects of Co2+, Ni2+, and Zn2+ on SARS-CoV-2 nsp15. Furthermore, the Co2+- or Ni2+-dependent activation of nsp15 is inhibited upon Zn2+ addition, suggesting competitive regulation. Overall, our work identifies the activator and inhibitor ions of nsp15 and suggests a metal-dependent regulatory mechanism of nsp15 activity.

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Organizational Affiliation: 
• Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China.
Department of Cardiology, Taikang Center for Life and Medical Sciences, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan430072, China.
Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen518063, China.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 252.47 kDa 
• Atom Count: 16,978 
• Modeled Residue Count: 2,051 
• Deposited Residue Count: 2,138 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridylate-specific endoribonuclease nsp15	A, B, C, D, E, F	346	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 4.6.1
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (31-MER)	G	31	Severe acute respiratory syndrome coronavirus 2

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (31-MER)	H	31	Severe acute respiratory syndrome coronavirus 2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO (Subject of Investigation/LOI)	I [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-11 
Deposition Author(s): Wang, L., Li, J., Zhu, B., Wang, X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-02-11
  Type: Initial release
  
• Version 1.1: 2026-08-26
  Changes: Data collection, Database references