1TG8 | pdb_00001tg8

The structure of Dengue virus E glycoprotein

• PDB DOI: https://doi.org/10.2210/pdb1TG8/pdb

• Classification: VIRAL PROTEIN
• Organism(s): dengue virus type 2
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2004-05-28 Released: 2004-09-28 
• Deposition Author(s): Zhang, Y., Zhang, W., Ogata, S., Clements, D., Strauss, J.H., Baker, T.S., Rossmann, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.294 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.264 (Depositor), 0.259 (DCC) 
• R-Value Observed: 
  0.264 (Depositor) 

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.31 kDa 
• Atom Count: 3,276 
• Modeled Residue Count: 390 
• Deposited Residue Count: 395 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
envelope glycoprotein	A	395	dengue virus type 2	Mutation(s): 0
UniProt
Find proteins for P27914 (Dengue virus type 2 (strain Tonga/EKB194/1974)) Explore P27914  Go to UniProtKB:  P27914

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	B [auth A], C [auth A]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.294 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.264 (Depositor), 0.259 (DCC) 
• R-Value Observed: 0.264 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.919	α = 90
b = 71.919	β = 90
c = 140.856	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

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., 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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary