8Y3J | pdb_00008y3j

Cryo-EM structure of dengue virus serotype 2 strain D2Y98P-PP1 at 4 deg C

• PDB DOI: https://doi.org/10.2210/pdb8Y3J/pdb
• EM Map EMD-38884: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): dengue virus type 2
• Expression System: Aedes albopictus
• Mutation(s): No 


• Deposited: 2024-01-29 Released: 2025-01-29 
• Deposition Author(s): Fibriansah, G., Ng, T.S., Lim, X.N., Tan, A.W.K., Shi, J., Lok, S.M.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Role of N-glycosylation at asparagine 153 of dengue envelope protein in immune response

Fibriansah, G., Ng, T.S., Lim, X.N., Tan, A.W.K., Shi, J., Crowe, J.E., Lok, S.M.

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: 189.95 kDa 
• Atom Count: 13,281 
• Modeled Residue Count: 1,710 
• Deposited Residue Count: 1,710 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein	A, C, E	495	dengue virus type 2	Mutation(s): 0  Gene Names: E
UniProt
Find proteins for A0A0S2PZC9 (dengue virus type 2) Explore A0A0S2PZC9  Go to UniProtKB:  A0A0S2PZC9
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane polyprotein	B, D, F	75	dengue virus type 2	Mutation(s): 0
UniProt
Find proteins for A4GVG9 (dengue virus type 2) Explore A4GVG9  Go to UniProtKB:  A4GVG9

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth C], 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: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Fibriansah, G., Ng, T.S., Lim, X.N., Tan, A.W.K., Shi, J., Lok, S.M.

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Funding Organization	Location	Grant Number
Other government	Singapore	MOH-OFIRG18may-0007

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release