3J42 | pdb_00003j42

Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 21.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history

Literature

Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody.

Wang, Z.Li, L.Pennington, J.G.Sheng, J.Yap, M.L.Plevka, P.Meng, G.Sun, L.Jiang, W.Rossmann, M.G.

(2013) J Virol 87: 8909-8915

  • DOI: https://doi.org/10.1128/JVI.00472-13
  • Primary Citation Related Structures: 
    3J42, 4KVC

  • PubMed Abstract: 

    The 2H2 monoclonal antibody recognizes the precursor peptide on immature dengue virus and might therefore be a useful tool for investigating the conformational change that occurs when the immature virus enters an acidic environment. During dengue virus maturation, spiky, immature, noninfectious virions change their structure to form smooth-surfaced particles in the slightly acidic environment of the trans-Golgi network, thereby allowing cellular furin to cleave the precursor-membrane proteins. The dengue virions become fully infectious when they release the cleaved precursor peptide upon reaching the neutral-pH environment of the extracellular space. Here we report on the cryo-electron microscopy structures of the immature virus complexed with the 2H2 antigen binding fragments (Fab) at different concentrations and under various pH conditions. At neutral pH and a high concentration of Fab molecules, three Fab molecules bind to three precursor-membrane proteins on each spike of the immature virus. However, at a low concentration of Fab molecules and pH 7.0, only two Fab molecules bind to each spike. Changing to a slightly acidic pH caused no detectable change of structure for the sample with a high Fab concentration but caused severe structural damage to the low-concentration sample. Therefore, the 2H2 Fab inhibits the maturation process of immature dengue virus when Fab molecules are present at a high concentration, because the three Fab molecules on each spike hold the precursor-membrane molecules together, thereby inhibiting the normal conformational change that occurs during maturation.


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

Macromolecule Content 

  • Total Structure Weight: 299.14 kDa 
  • Atom Count: 11,226 
  • Modeled Residue Count: 2,697 
  • Deposited Residue Count: 2,712 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope protein E
A, B, C
390dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for A7TUD3 (Dengue virus type 2)
Explore A7TUD3 
Go to UniProtKB:  A7TUD3
Entity Groups
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UniProt GroupA7TUD3
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PrM
D, E, F
81dengue virus type 2Mutation(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
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Ig heavy chain V region MOPC 21, Igh protein chimera
G, I, K
221Mus musculusMutation(s): 0 
Gene Names: Igh-1aIgh
UniProt
Find proteins for P01865 (Mus musculus)
Explore P01865 
Go to UniProtKB:  P01865
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UniProt GroupP01865
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Ig kappa chain V-V region MOPC 21, Anti-colorectal carcinoma light chain chimera
H, J, L
212Mus musculusMutation(s): 0 
Gene Names: Gm16939
UniProt
Find proteins for P01837 (Mus musculus)
Explore P01837 
Go to UniProtKB:  P01837
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UniProt GroupP01837
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 21.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN1
RECONSTRUCTIONEMAN2
RECONSTRUCTIONjspr

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-08-14
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection
  • Version 1.3: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary