8JN4

Cryo-EM structure of dengue virus serotype 3 strain 863DK in complex with human antibody DENV-290 Fab at 4 deg C (subparticle LLR-LRR)

• PDB DOI: https://doi.org/10.2210/pdb8JN4/pdb
• EM Map EMD-36432: EMDB EMDataResource

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


• Deposited: 2023-06-06 Released: 2024-06-12 
• Deposition Author(s): Fibriansah, G., Ng, T.S., Tan, A.W.K., Shi, J., Lok, S.M.
• Funding Organization(s): National Research Foundation (NRF, Singapore)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Ultrapotent human antibodies lock E protein dimers of diverse DENV3 morphological variants

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 16-mer - A6B6C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 16-mer - A6B6C4 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 215.97 kDa 
• Atom Count: 15,113 
• Modelled Residue Count: 1,939 
• Deposited Residue Count: 1,939 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein	A, C, E	493	dengue virus type 3	Mutation(s): 0
UniProt
Find proteins for A9LIF4 (dengue virus type 3) Explore A9LIF4  Go to UniProtKB:  A9LIF4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane protein	B, D, F	75	dengue virus type 3	Mutation(s): 0
UniProt
Find proteins for M1J7M3 (dengue virus type 3) Explore M1J7M3  Go to UniProtKB:  M1J7M3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Human antibody DENV-290 heavy chain	G [auth H]	122	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Human antibody DENV-290 light chain	H [auth L]	113	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth G], K [auth J]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G51945PF GlyCosmos:  G51945PF GlyGen:  G51945PF

Entity ID: 6
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	J [auth I], L [auth K], N	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 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: 2024-06-12 
Deposition Author(s): Fibriansah, G., Ng, T.S., Tan, A.W.K., Shi, J., Lok, S.M.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Singapore)	Singapore	NRF-NRFI2016-01

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release