8JN1

Cryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C (subparticle LLR-LRR)

• PDB DOI: https://doi.org/10.2210/pdb8JN1/pdb
• EM Map EMD-36429: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): dengue virus type 3, Homo sapiens
• Expression System: Aedes albopictus, Homo sapiens
• Mutation(s): Yes 


• 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 

Starting Models: experimental

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: 214.27 kDa 
• Atom Count: 14,985 
• Modelled Residue Count: 1,935 
• Deposited Residue Count: 1,936 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein (Fragment)	A, C, E	493	dengue virus type 3	Mutation(s): 0
UniProt
Find proteins for A0A3G1J4X7 (dengue virus type 3) Explore A0A3G1J4X7  Go to UniProtKB:  A0A3G1J4X7
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	B, D, F	75	dengue virus type 3	Mutation(s): 1  Gene Names: PrM/M, E
UniProt
Find proteins for A0A7D0UCF5 (dengue virus type 3) Explore A0A7D0UCF5  Go to UniProtKB:  A0A7D0UCF5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Human antibody DENV-115 heavy chain	G [auth H]	122	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Human antibody DENV-115 light chain	H [auth L]	110	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth G], J [auth I], K [auth J], N	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

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	L [auth K], M	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

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
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Structure summary