5IY3 | pdb_00005iy3

Zika Virus Non-structural Protein NS1

• PDB DOI: https://doi.org/10.2210/pdb5IY3/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Zika virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-23 Released: 2016-04-13 
• Deposition Author(s): Song, H., Qi, J., Shi, Y., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Zika virus NS1 structure reveals diversity of electrostatic surfaces among flaviviruses

Song, H., Qi, J., Haywood, J., Shi, Y., Gao, G.F.

(2016) Nat Struct Mol Biol 23: 456-458

• PubMed: 27088990 
• DOI: https://doi.org/10.1038/nsmb.3213
• Primary Citation of Related Structures:  
  5IY3


• PubMed Abstract: 
  

  The association of Zika virus (ZIKV) infections with microcephaly has resulted in an ongoing public-health emergency. Here we report the crystal structure of a C-terminal fragment of ZIKV nonstructural protein 1 (NS1), a major host-interaction molecule that functions in flaviviral replication, pathogenesis and immune evasion. Comparison with West Nile and dengue virus NS1 structures reveals conserved features but diverse electrostatic characteristics at host-interaction interfaces, thus possibly implying different modes of flavivirus pathogenesis.

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Organizational Affiliation: 

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.53 kDa 
• Atom Count: 2,899 
• Modelled Residue Count: 354 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	181	Zika virus	Mutation(s): 0
UniProt
Find proteins for A0A109PRQ3 (Zika virus) Explore A0A109PRQ3  Go to UniProtKB:  A0A109PRQ3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.868	α = 90
b = 103.755	β = 90
c = 114.843	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Song, H., Qi, J., Shi, Y., Gao, G.F.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2016-04-20
  Changes: Database references
• Version 1.2: 2016-04-27
  Changes: Database references
• Version 1.3: 2016-05-25
  Changes: Database references
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary