9M49 | pdb_00009m49

Cryo-EM structure of 6:2 nsp15/dsRNA complex

• PDB DOI: https://doi.org/10.2210/pdb9M49/pdb
• EM Map EMD-63619: 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: 2.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Coronavirus nsp15 is activated by Co2+ and Ni2+ while inhibited by Zn2+

Wang, X., Li, J., Wang, L., Zhu, B.

To be published.

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: 272.23 kDa 
• Atom Count: 18,287 
• Modeled Residue Count: 2,113 
• Deposited Residue Count: 2,200 
• 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 [auth C], C [auth E], D [auth F], I [auth B], J [auth D]	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)	E [auth G], G [auth I]	31	Severe acute respiratory syndrome coronavirus 2

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (31-MER)	F [auth H], H [auth J]	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)	K [auth G], L [auth I]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.78 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