9XH4 | pdb_00009xh4

Cryo-EM structure of unnatural-base aptamer AptD1 with DENV1 NS1 hexamer

PDB DOI: https://doi.org/10.2210/pdb9XH4/pdb
EM Map EMD-66866: EMDB EMDataResource

Classification: VIRAL PROTEIN/DNA
Organism(s): Dengue virus 1 Nauru/West Pac/1974, 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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.72 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 302.36 kDa
Atom Count: 18,918
Modeled Residue Count: 2,205
Deposited Residue Count: 2,364
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 1	A C [auth B] D [auth C] F [auth E] G [auth F] A, C [auth B], D [auth C], F [auth E], G [auth F], I	370	Dengue virus 1 Nauru/West Pac/1974	Mutation(s): 0
UniProt
Find proteins for P17763 (Dengue virus type 1 (strain Nauru/West Pac/1974)) Explore P17763 Go to UniProtKB: P17763
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17763
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
unnatural-base aptamer AptD1	B [auth G], E [auth D], H	48	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLC Query on PLC Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain Q [auth E] SDF format, chain V [auth I] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth E] MOL2 format, chain V [auth I] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth E] mmCIF format, chain V [auth I]	L [auth B], Q [auth E], V [auth I]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain L [auth B] Focus chain Q [auth E] Focus chain V [auth I] Interactions & Density Focus chain L [auth B] Focus chain Q [auth E] Focus chain V [auth I]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain T [auth F] SDF format, chain U [auth F] SDF format, chain W [auth I] SDF format, chain X [auth I] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] MOL2 format, chain W [auth I] MOL2 format, chain X [auth I] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F] mmCIF format, chain W [auth I] mmCIF format, chain X [auth I]	J [auth A] K [auth A] M [auth B] N [auth B] O [auth C] J [auth A], K [auth A], M [auth B], N [auth B], O [auth C], P [auth C], R [auth E], S [auth E], T [auth F], U [auth F], W [auth I], X [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain W [auth I] Focus chain X [auth I] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain W [auth I] Focus chain X [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.72 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

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

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