1THD | pdb_00001thd

COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5 ANGSTROM CRYO-EM RECONSTRUCTION

• PDB DOI: https://doi.org/10.2210/pdb1THD/pdb

• Classification: VIRUS
• Organism(s): Dengue virus 2 Puerto Rico/PR159-S1/1969
• Mutation(s): No 


• Deposited: 2004-06-01 Released: 2004-09-28 
• Deposition Author(s): Zhang, Y., Zhang, W., Ogata, S., Clements, D., Strauss, J.H., Baker, T.S., Kuhn, R.J., Rossmann, M.G.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 9.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Conformational changes of the flavivirus e glycoprotein

Zhang, Y., Zhang, W., Ogata, S., Clements, D., Strauss, J.H., Baker, T.S., Kuhn, R.J., Rossmann, M.G.

(2004) Structure 12: 1607-1618

• PubMed: 15341726 
• DOI: https://doi.org/10.1016/j.str.2004.06.019
• Primary Citation Related Structures: 
  1TG8, 1TGE, 1THD


• PubMed Abstract: 
  

  Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal fragment of E has been determined and compared with a previously described structure. The primary difference between these structures is a 10 degrees rotation about a hinge relating the fusion domain DII to domains DI and DIII. These two rigid body components were used for independent fitting of E into the cryo-electron microscopy maps of both immature and mature dengue viruses. The fitted E structures in these two particles showed a difference of 27 degrees between the two components. Comparison of the E structure in its postfusion state with that in the immature and mature virions shows a rotation approximately around the same hinge. Flexibility of E is apparently a functional requirement for assembly and infection of flaviviruses.

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Organizational Affiliation: 
• Department of Biological Sciences, Lilly Hall, 915 West State Street, Purdue University, West Lafayette, IN 47907, USA.

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: 131.59 kDa 
• Atom Count: 1,170 
• Modeled Residue Count: 1,170 
• 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	Dengue virus 2 Puerto Rico/PR159-S1/1969	Mutation(s): 0
UniProt
Find proteins for P12823 (Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969)) Explore P12823  Go to UniProtKB:  P12823

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 9.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	POR

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-28 
Deposition Author(s): Zhang, Y., Zhang, W., Ogata, S., Clements, D., Strauss, J.H., Baker, T.S., Kuhn, R.J., Rossmann, M.G.

Revision History  

• Version 1.0: 2004-09-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description