9OWE | pdb_00009owe

CryoEM structure of stabilized dengue 3 virus envelope glycoprotein in complex with Fab of F25.S02

• PDB DOI: https://doi.org/10.2210/pdb9OWE/pdb
• EM Map EMD-70931: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): dengue virus type 3, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-06-02 Released: 2026-03-04 
• Deposition Author(s): Hurlburt, N.K., Pancera, M.
• Funding Organization(s): Other private

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for antibody cross-neutralization of dengue and Zika viruses

Hurlburt, N.K., Pancera, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 188.82 kDa 
• Atom Count: 9,706 
• Modeled Residue Count: 1,252 
• Deposited Residue Count: 1,722 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	406	dengue virus type 3	Mutation(s): 0
UniProt
Find proteins for Q07019 (Dengue virus type 3) Explore Q07019  Go to UniProtKB:  Q07019
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F25.S02 Heavy chain	C, E [auth H]	238	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
F25.S02 Light chain	D, F [auth L]	217	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth E], H [auth F]	3		N-Glycosylation

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	C, E [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-04 
Deposition Author(s): Hurlburt, N.K., Pancera, M.

---

Funding Organization	Location	Grant Number
Other private		Fred Hutchinson Cancer Center

Revision History  

• Version 1.0: 2026-03-04
  Type: Initial release