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



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