5TMH

Structure of Zika virus NS5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.264 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/ncomms14763
  • Primary Citation of Related Structures:  
    5TMH

  • 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-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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyprotein
A, B
902Zika virusMutation(s): 0 
UniProt
Find proteins for Q32ZE1 (Zika virus)
Explore Q32ZE1 
Go to UniProtKB:  Q32ZE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ32ZE1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth B],
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.264 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.136α = 90
b = 136.478β = 90
c = 196.978γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references