5TMH

Structure of Zika virus NS5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.278 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The structure of Zika virus NS5 reveals a conserved domain conformation.

Wang, B., Tan, X.F., Thurmond, S., Zhang, Z.M., Lin, A., Hai, R., Song, J.

(2017) Nat Commun 8: 14763-14763

  • DOI: 10.1038/ncomms14763

  • PubMed Abstract: 

    • The recent outbreak of Zika virus (ZIKV) has imposed a serious threat to public health. Here we report the crystal structure of the ZIKV NS5 protein in complex with S-adenosyl-L-homocysteine, in which the tandem methyltransferase (MTase) and RNA-depe ...

    The recent outbreak of Zika virus (ZIKV) has imposed a serious threat to public health. Here we report the crystal structure of the ZIKV NS5 protein in complex with S-adenosyl-L-homocysteine, in which the tandem methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains stack into one of the two alternative conformations of flavivirus NS5 proteins. The activity of this NS5 protein is verified through a de novo RdRp assay on a subgenomic ZIKV RNA template. Importantly, our structural analysis leads to the identification of a potential drug-binding site of ZIKV NS5, which might facilitate the development of novel antivirals for ZIKV.

    Organizational Affiliation: 

    Department of Biochemistry, University of California, Riverside, Riverside, California 92521, USA.,Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, California 92521, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyprotein
A, B
902Zika virusMutation(s): 0 
Find proteins for Q32ZE1 (Zika virus)
Go to UniProtKB:  Q32ZE1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH
Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.278 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.262 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 95.136α = 90.00
b = 136.478β = 90.00
c = 196.978γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description
  • Version 1.2: 2019-07-31
    Type: Data collection, Database references