5GS6

Full-length NS1 structure of Zika virus from 2015 Brazil strain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Contribution of intertwined loop to membrane association revealed by Zika virus full-length NS1 structure

Xu, X.Song, H.Qi, J.Liu, Y.Wang, H.Su, C.Shi, Y.Gao, G.F.

(2016) EMBO J 35: 2170-2178

  • DOI: https://doi.org/10.15252/embj.201695290
  • Primary Citation of Related Structures:  
    5GS6

  • PubMed Abstract: 

    The association of Zika virus (ZIKV) infections with microcephaly and neurological diseases has highlighted an emerging public health concern. Here, we report the crystal structure of the full-length ZIKV nonstructural protein 1 (NS1), a major host-interaction molecule that functions in flaviviral replication, pathogenesis, and immune evasion. Of note, a long intertwined loop is observed in the wing domain of ZIKV NS1, and forms a hydrophobic "spike", which can contribute to cellular membrane association. For different flaviviruses, the amino acid sequences of the "spike" are variable but their common characteristic is either hydrophobic or positively charged, which is a beneficial feature for membrane binding. Comparative studies with West Nile and Dengue virus NS1 structures reveal conserved features, but diversified electrostatic characteristics on both inner and outer faces. Our results suggest different mechanisms of flavivirus pathogenesis and should be considered during the development of diagnostic tools.


  • Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Hefei, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NS1 of Zika virus from 2015 Brazil strain
A, B
357Zika virusMutation(s): 0 
Gene Names: NS1
UniProt
Find proteins for A0A109PRQ3 (Zika virus)
Explore A0A109PRQ3 
Go to UniProtKB:  A0A109PRQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A109PRQ3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.948α = 90
b = 96.948β = 90
c = 270.143γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-03-20
    Changes: Source and taxonomy