4B03

6A Electron cryomicroscopy structure of immature Dengue virus serotype 1

• PDB DOI: https://doi.org/10.2210/pdb4B03/pdb
• EM Map EMD-2141: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): dengue virus type 1
• Mutation(s): No 


• Deposited: 2012-06-28 Released: 2013-06-05 
• Deposition Author(s): Kostyuchenko, V.A., Zhang, Q., Tan, L.C., Ng, T.S., Lok, S.M.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Immature and Mature Dengue Serotype 1 Virus Structures Provide Insight Into the Maturation Process.

Kostyuchenko, V.A., Zhang, Q., Tan, J.L., Ng, T.S., Lok, S.M.

(2013) J Virol 87: 7700

• PubMed: 23637416 
• DOI: https://doi.org/10.1128/JVI.00197-13
• Primary Citation of Related Structures:  
  4B03, 4CCT


• PubMed Abstract: 
  

  Dengue virus is a major human pathogen that has four serotypes (DENV1 to -4). Here we report the cryoelectron microscopy (cryo-EM) structures of immature and mature DENV1 at 6- and 4.5-Å resolution, respectively. The subnanometer-resolution maps allow accurate placement of all of the surface proteins. Although the immature and mature viruses showed vastly different surface protein organizations, the envelope protein transmembrane (E-TM) regions remain in similar positions. The pivotal role of the E-TM regions leads to the identification of the start and end positions of all surface proteins during maturation.

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Organizational Affiliation: 

Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 360-mer - A180B180 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 216.96 kDa 
• Atom Count: 1,983 
• Modelled Residue Count: 1,983 
• Deposited Residue Count: 1,983 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DENGUE VIRUS 1 E PROTEIN	A, B, C	495	dengue virus type 1	Mutation(s): 0
UniProt
Find proteins for G3F5K5 (dengue virus type 1) Explore G3F5K5  Go to UniProtKB:  G3F5K5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DENGUE VIRUS 1 PRM PROTEIN	D, E, F	166	dengue virus type 1	Mutation(s): 0
UniProt
Find proteins for G3F5K5 (dengue virus type 1) Explore G3F5K5  Go to UniProtKB:  G3F5K5

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN	1
RECONSTRUCTION	EMAN	2

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-05 
Deposition Author(s): Kostyuchenko, V.A., Zhang, Q., Tan, L.C., Ng, T.S., Lok, S.M.

Revision History  

• Version 1.0: 2013-06-05
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references
• Version 1.2: 2017-04-19
  Changes: Other
• Version 1.3: 2017-08-30
  Changes: Data collection
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Refinement description