8JN6

Cryo-EM structure of the small tail club shape particle of dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg C

• PDB DOI: https://doi.org/10.2210/pdb8JN6/pdb
• EM Map EMD-36434: 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: 9.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: HELICAL 

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: Helical - H  (Explore in 3D)
Global Stoichiometry: Hetero 92-mer - A46B23C23 Pseudo Symmetry: Helical - H  (Explore in 3D)
Pseudo Stoichiometry: Hetero 92-mer - A46B46 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 133.34 kDa 
• Atom Count: 1,256 
• Modelled Residue Count: 1,022 
• Deposited Residue Count: 1,221 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein (Fragment)	A [auth C], B [auth E]	493	dengue virus type 3	Mutation(s): 0
UniProt
Find proteins for Q07019 (dengue virus type 3) Explore Q07019  Go to UniProtKB:  Q07019

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human antibody DENV-290 heavy chain	C [auth H]	122	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Human antibody DENV-290 light chain	D [auth L]	113	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 9.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: HELICAL 

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