9MVC | pdb_00009mvc

DENV3 mature structure at 4 degree Celsius

• PDB DOI: https://doi.org/10.2210/pdb9MVC/pdb
• EM Map EMD-48664: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): dengue virus type 3
• Expression System: Aedes albopictus
• Mutation(s): No 


• Deposited: 2025-01-15 Released: 2026-07-22 
• Deposition Author(s): Are, V.N., Fokine, A., Klose, T., Kuhn, R.J., Center for Structural Biology of Infectious Diseases (CSBID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures and biochemical assays demonstrate dengue viruses utilize heparin and glycan binding receptor DC-SIGN for infection

Are, V.N., Kuhn, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 360-mer - A180B180 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 187.42 kDa 
• Atom Count: 13,116 
• Modeled Residue Count: 1,704 
• Deposited Residue Count: 1,704 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein E	A, C, E	493	dengue virus type 3	Mutation(s): 0
UniProt
Find proteins for Q6DRA0 (Dengue virus type 3) Explore Q6DRA0  Go to UniProtKB:  Q6DRA0
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
M protein	B, D, F	75	dengue virus type 3	Mutation(s): 0
UniProt
Find proteins for Q6DRA0 (Dengue virus type 3) Explore Q6DRA0  Go to UniProtKB:  Q6DRA0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth C], J [auth C], K [auth E], L [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-22 
Deposition Author(s): Are, V.N., Fokine, A., Klose, T., Kuhn, R.J., Center for Structural Biology of Infectious Diseases (CSBID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U01 AI11001613

Revision History  

• Version 1.0: 2026-07-22
  Type: Initial release