8ZBF | pdb_00008zbf

Crystal structure of the A58-T10 DNA aptamer in complex with SARS-CoV-2 N-NTD

• PDB DOI: https://doi.org/10.2210/pdb8ZBF/pdb
• NAKB: 8ZBF

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


• Deposited: 2024-04-26 Released: 2025-04-30 
• Deposition Author(s): Chen, X., Huang, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Models: experimental, integrative

Literature

Molecular characterization and broad-spectrum mechanism of coronavirus N protein aptamer

Chen, X., Huang, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 108.78 kDa 
• Atom Count: 7,034 
• Modeled Residue Count: 646 
• Deposited Residue Count: 700 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B, C, D	135	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: N
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9  Go to UniProtKB:  P0DTC9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (40-MER)	E, F, G, H	40	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA (Subject of Investigation/LOI)	I [auth A], J [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.97	α = 90
b = 92.48	β = 90.54
c = 77.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Chen, X., Huang, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171191
Other private		YXQH202418

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release
  
• Version 1.1: 2025-05-07
  Changes: Experimental preparation