9XHA | pdb_00009xha

Cryo-EM structure of unnatural-base aptamer AptD2 with DENV2 NS1

• PDB DOI: https://doi.org/10.2210/pdb9XHA/pdb
• EM Map EMD-66871: EMDB EMDataResource

• Classification: VIRAL PROTEIN/DNA
• Organism(s): Dengue virus 2 Thailand/16681/84, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-10-31 Released: 2026-11-04 
• Deposition Author(s): Sawada, K., Sano, F.K., Shuto, Y., Hirano, H., Kusakizako, T., Itoh, Y., Kise, Y., Nureki, O.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Insights into Enhanced Binding Affinity and Specificity of Six-Letter DNA Aptamers to Dengue Antigen NS1 Proteins via Genetic Alphabet Expansion

Sawada, K., Kimoto, M., Matsunaga, K., Tan, H.P., Takayanagi, R., Sano, F.K., Shuto, Y., Hirano, H., Kusakizako, T., Itoh, Y., Kise, Y., Hirao, I., Nureki, O.

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.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 107.27 kDa 
• Atom Count: 6,327 
• Modeled Residue Count: 717 
• Deposited Residue Count: 812 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 1	A, C [auth B]	370	Dengue virus 2 Thailand/16681/84	Mutation(s): 0
UniProt
Find proteins for P29990 (Dengue virus type 2 (strain Thailand/16681/1984)) Explore P29990  Go to UniProtKB:  P29990
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
unnatural-base aptamer AptD2	B [auth C]	72	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.39 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-04 
Deposition Author(s): Sawada, K., Sano, F.K., Shuto, Y., Hirano, H., Kusakizako, T., Itoh, Y., Kise, Y., Nureki, O.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP223fa627001
Japan Agency for Medical Research and Development (AMED)	Japan	JP19am0401005
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121002
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121012
Japan Science and Technology	Japan	JPMJCR20E2
Japan Science and Technology	Japan	JPMJPR22E4
Japan Society for the Promotion of Science (JSPS)	Japan	JP20K15754
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K15072
Japan Society for the Promotion of Science (JSPS)	Japan	JP24K01961
Japan Society for the Promotion of Science (JSPS)	Japan	JP25KJ0866
Japan Society for the Promotion of Science (JSPS)	Japan	JP23KJ0491
Japan Agency for Medical Research and Development (AMED)	Japan	JP25gm7110004
Japan Agency for Medical Research and Development (AMED)	Japan	JP223fa627001

Revision History  

• Version 1.0: 2026-11-04
  Type: Initial release