2I69

Crystal structure of the West Nile virus envelope glycoprotein

• PDB DOI: https://doi.org/10.2210/pdb2I69/pdb

• Classification: VIRAL PROTEIN
• Organism(s): West Nile virus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2006-08-28 Released: 2006-11-21 
• Deposition Author(s): Kanai, R., Modis, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.268 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.07 kDa 
• Atom Count: 3,095 
• Modelled Residue Count: 403 
• Deposited Residue Count: 403 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	A	403	West Nile virus	Mutation(s): 0  Gene Names: Envelope protein Membrane Entity: Yes
UniProt
Find proteins for Q80QJ9 (West Nile virus) Explore Q80QJ9  Go to UniProtKB:  Q80QJ9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G28454KX GlyCosmos:  G28454KX GlyGen:  G28454KX

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.268 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.262	α = 90
b = 93.262	β = 90
c = 159.319	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): Kanai, R., Modis, Y.

Revision History  

• Version 1.0: 2006-11-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary