Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 207.60 kDa 
• Atom Count: 13429 
• Modelled Residue Count: 1760 
• Deposited Residue Count: 1804 
• Unique protein chains: 1

5TMH

Structure of Zika virus NS5

• PDB DOI: 10.2210/pdb5TMH/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Zika virus
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2016-10-12 Released: 2017-02-08 
• Deposition Author(s): Wang, B., Tan, X., Song, J.

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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 

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

• PubMed: 28345600 
• DOI: 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.

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Organizational Affiliation: 

Department of Biochemistry, University of California, Riverside, Riverside, California 92521, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyprotein	A, B	902	Zika virus	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1  Go to UniProtKB:  Q32ZE1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], I [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SO4	F [auth A], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	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 = 95.136	α = 90
b = 136.478	β = 90
c = 196.978	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-10-12 
• Released Date: 2017-02-08 
Deposition Author(s): Wang, B., Tan, X., Song, J.

Revision History  

• 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