1K4R | pdb_00001k4r

Structure of Dengue Virus

• PDB DOI: https://doi.org/10.2210/pdb1K4R/pdb

• Classification: VIRUS
• Organism(s): Chimeric Tick-borne encephalitis virus/Dengue virus 4
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2001-10-08 Released: 2002-03-13 
• Deposition Author(s): Kuhn, R.J., Zhang, W., Rossmann, M.G., Pletnev, S.V., Corver, J., Lenches, E., Jones, C.T., Mukhopadhyay, S., Chipman, P.R., Strauss, E.G., Baker, T.S., Strauss, J.H.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 24.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structure of dengue virus: implications for flavivirus organization, maturation, and fusion.

Kuhn, R.J., Zhang, W., Rossmann, M.G., Pletnev, S.V., Corver, J., Lenches, E., Jones, C.T., Mukhopadhyay, S., Chipman, P.R., Strauss, E.G., Baker, T.S., Strauss, J.H.

(2002) Cell 108: 717-725

• PubMed: 11893341 
• DOI: https://doi.org/10.1016/s0092-8674(02)00660-8
• Primary Citation Related Structures: 
  1K4R


• PubMed Abstract: 
  

  The first structure of a flavivirus has been determined by using a combination of cryoelectron microscopy and fitting of the known structure of glycoprotein E into the electron density map. The virus core, within a lipid bilayer, has a less-ordered structure than the external, icosahedral scaffold of 90 glycoprotein E dimers. The three E monomers per icosahedral asymmetric unit do not have quasiequivalent symmetric environments. Difference maps indicate the location of the small membrane protein M relative to the overlaying scaffold of E dimers. The structure suggests that flaviviruses, and by analogy also alphaviruses, employ a fusion mechanism in which the distal beta barrels of domain II of the glycoprotein E are inserted into the cellular membrane.

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Organizational Affiliation: 
• Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 180-mer - A180 

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

Macromolecule Content 

• Total Structure Weight: 129.69 kDa 
• Atom Count: 9,084 
• Modeled Residue Count: 1,185 
• Deposited Residue Count: 1,185 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR ENVELOPE PROTEIN E	A, B, C	395	Chimeric Tick-borne encephalitis virus/Dengue virus 4	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P14336 (Tick-borne encephalitis virus European subtype (strain Neudoerfl)) Explore P14336  Go to UniProtKB:  P14336

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 24.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	OTHER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-03-13 
Deposition Author(s): Kuhn, R.J., Zhang, W., Rossmann, M.G., Pletnev, S.V., Corver, J., Lenches, E., Jones, C.T., Mukhopadhyay, S., Chipman, P.R., Strauss, E.G., Baker, T.S., Strauss, J.H.

Revision History  

• Version 1.0: 2002-03-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-07-18
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary