1OAN

Crystal structure of the dengue 2 virus envelope protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 

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Literature

A Ligand-Binding Pocket in the Dengue Virus Envelope Glycoprotein

Modis, Y., Ogata, S., Clements, D., Harrison, S.C.

(2003) Proc Natl Acad Sci U S A 100: 6986

  • DOI: 10.1073/pnas.0832193100
  • Primary Citation of Related Structures:  
    1OAN, 1OKE

  • PubMed Abstract: 

    • Dengue virus is an emerging global health threat. Its major envelope glycoprotein, E, mediates viral attachment and entry by membrane fusion. A crystal structure of the soluble ectodomain of E from dengue virus type 2 reveals a hydrophobic pocket lined by residues that influence the pH threshold for fusion ...

    Dengue virus is an emerging global health threat. Its major envelope glycoprotein, E, mediates viral attachment and entry by membrane fusion. A crystal structure of the soluble ectodomain of E from dengue virus type 2 reveals a hydrophobic pocket lined by residues that influence the pH threshold for fusion. The pocket, which accepts a hydrophobic ligand, opens and closes through a conformational shift in a beta-hairpin at the interface between two domains. These features point to a structural pathway for the fusion-activating transition and suggest a strategy for finding small-molecule inhibitors of dengue and other flaviviruses.

    Related Citations: 
    • The Envelope Glycoprotein from Tick-Borne Encephalitis Virus at 2 A Resolution
      Rey, F.A., Heinz, F.X., Mandl, C., Kunz, C., Harrison, S.C.
      (1995) Nature 375: 291
    Organizational Affiliation: 

    Howard Hughes Medical Institute, Children's Hospital and Harvard Medical School, 320 Longwood Avenue, Boston, MA 02115, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENVELOPE GLYCOPROTEINA, B394Dengue virus 2Mutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P12823 (Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969))
Explore P12823 
Go to UniProtKB:  P12823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12823
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseC, D 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
F [auth A],
G [auth B]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.541α = 90
b = 81.541β = 90
c = 288.623γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    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, Other, Structure summary