3J8D

Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 26.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of Acidic pH Dengue Virus Showing the Fusogenic Glycoprotein Trimers.

Zhang, X.Sheng, J.Austin, S.K.Hoornweg, T.E.Smit, J.M.Kuhn, R.J.Diamond, M.S.Rossmann, M.G.

(2015) J Virol 89: 743-750

  • DOI: https://doi.org/10.1128/JVI.02411-14
  • Primary Citation of Related Structures:  
    3J8D

  • PubMed Abstract: 

    Flaviviruses undergo large conformational changes during their life cycle. Under acidic pH conditions, the mature virus forms transient fusogenic trimers of E glycoproteins that engage the lipid membrane in host cells to initiate viral fusion and nucleocapsid penetration into the cytoplasm. However, the dynamic nature of the fusogenic trimer has made the determination of its structure a challenge. Here we have used Fab fragments of the neutralizing antibody DV2-E104 to stop the conformational change of dengue virus at an intermediate stage of the fusion process. Using cryo-electron microscopy, we show that in this intermediate stage, the E glycoproteins form 60 trimers that are similar to the predicted "open" fusogenic trimer.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
glycoprotein DIIIA [auth B],
D [auth F]
97Dengue virus 2 Thailand/16681/84Mutation(s): 0 
UniProt
Find proteins for P17763 (Dengue virus type 1 (strain Nauru/West Pac/1974))
Explore P17763 
Go to UniProtKB:  P17763
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UniProt GroupP17763
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
antibody E111 Fab fragmentB [auth A],
C [auth D]
425Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope protein EE [auth G],
F [auth H],
G [auth I]
394Dengue virus 2 Thailand/16681/84Mutation(s): 0 
UniProt
Find proteins for P29990 (Dengue virus type 2 (strain Thailand/16681/1984))
Explore P29990 
Go to UniProtKB:  P29990
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UniProt GroupP29990
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 26.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Source and taxonomy
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description