8JN7 | pdb_00008jn7

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Ultrapotent human antibodies lock E protein dimers central region 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 Jr., J.E.Lok, S.M.

(2025) Nat Commun 16: 9182-9182

  • DOI: https://doi.org/10.1038/s41467-025-64210-7
  • Primary Citation of Related Structures:  
    8JN1, 8JN2, 8JN3, 8JN4, 8JN5, 8JN6, 8JN7

  • PubMed Abstract: 

    Dengue virus (DENV) consists of four serotypes (DENV1-4). Current vaccines induce differing levels of immune response against the four serotypes, that might prime recipients to develop severe disease in subsequent infections. Several DENV tetravalent vaccine clinical trials suggested an increased incidence in severe DENV3 cases, suggesting a need to develop DENV3 therapeutics. Human monoclonal antibodies (HMAbs) DENV-290 and DENV-115 are ultrapotent against diverse DENV3 strains with differing particle morphologies. They mainly neutralize by inhibition of virus attachment to cells. CryoEM structures of Fabs complexed with differing DENV3 morphological variants show their Fabs binding across two E protein protomers at the center of the E dimer. This new class of E protein dimer binding antibodies is named EDE-C. The cryoEM structures also show how IgGs engage the DENV particles. Results define the structural and molecular basis for the ultrapotent activity of EDE-C antibodies.


  • Organizational Affiliation
    • Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyprotein (Fragment)A [auth C],
B [auth E]
493dengue virus type 3Mutation(s): 0 
UniProt
Find proteins for Q07019 (dengue virus type 3)
Explore Q07019 
Go to UniProtKB:  Q07019
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07019
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Human antibody DENV-290 heavy chainC [auth H]122Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Human antibody DENV-290 light chainD [auth L]113Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)SingaporeNRF-NRFI2016-01

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Data collection, Database references, Structure summary