5O36

Japanese encephalitis virus non-structural protein 1' C-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Study of the C-Terminal Domain of Nonstructural Protein 1 from Japanese Encephalitis Virus.

Poonsiri, T.Wright, G.S.A.Diamond, M.S.Turtle, L.Solomon, T.Antonyuk, S.V.

(2018) J. Virol. 92: --

  • DOI: 10.1128/JVI.01868-17
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Japanese encephalitis virus (JEV) is a mosquito-transmitted Flavivirus that is closely related to other emerging viral pathogens including dengue, West Nile (WNV) and Zika viruses. JEV infection can result in meningitis and encephalitis, which in sev ...

    Japanese encephalitis virus (JEV) is a mosquito-transmitted Flavivirus that is closely related to other emerging viral pathogens including dengue, West Nile (WNV) and Zika viruses. JEV infection can result in meningitis and encephalitis, which in severe cases cause permanent brain damage and death. JEV occurs predominantly in rural areas throughout Southeast Asia, the Pacific islands and the Far East, causing around 68,000 cases worldwide each year. In this study, we present a 2.1 Å resolution crystal structure of the C-terminal β-ladder domain of JEV non-structural protein 1 (NS1-C). The surface charge distribution of JEV NS1-C is similar to WNV and ZIKV but differs form DENV. Analysis of the JEV NS1-C structure, with in silico molecular dynamics simulation and experimental solution small angle X-ray scattering, indicates extensive loop flexibility on the exterior of the protein. This, together with the surface charge distribution, indicates flexibility influences the protein-protein interactions that govern pathogenicity. These factors also affect the interaction of NS1 with the monoclonal antibody, 22NS1, which is protective against West Nile virus infection. Liposome and heparin binding assays indicate that only the N-terminal region of NS1 mediates interaction with membranes, and that sulfate binding sites common to NS1 structures are not glycosaminoglycan binding interfaces. This study highlights several differences between flavivirus NS1 proteins and contributes to our understanding of their structure-pathogenic function relationships.IMPORTANCE JEV is a major cause of viral encephalitis in Asia. Despite extensive vaccination, epidemics still occur. Non-structural protein 1 (NS1) plays a role in viral replication and, because it is secreted, it can exhibit a wide range of interations with host proteins. NS1 sequence and protein folds are conserved within the Flavivirus genus, but variations in NS1 protein-protein interactions among viruses likely contribute to differences in pathogenesis. Here, we compared characteristics of the the C-terminal β-ladder domain of NS1 between flaviviruses including surface charge, loop flexibility, epitope cross-reactivity, membrane adherence, and glycosaminoglycan binding. These structural features are central to NS1 functionality and may provide insight into the development of diagnostic tests and therapeutics.


    Organizational Affiliation

    Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Japanese encephalitis virus non-structural protein 1' (NS1'),Japanese encephalitis virus non-structural protein 1' (NS1')
A
234Japanese encephalitis virus (strain SA-14)Mutation(s): 0 
Find proteins for P0DOH7 (Japanese encephalitis virus (strain SA-14))
Go to UniProtKB:  P0DOH7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POL
Query on POL

Download SDF File 
Download CCD File 
A
N-PROPANOL
1-PROPONOL
C3 H8 O
BDERNNFJNOPAEC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.167 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.320α = 90.00
b = 77.940β = 90.00
c = 163.490γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-01-31
    Type: Database references
  • Version 1.2: 2018-03-28
    Type: Database references