5GP1

Crystal structure of ZIKV NS5 Methyltransferase in complex with GTP and SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.444 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the NS5 methyltransferase from Zika virus and implications in inhibitor design

Zhang, C.Feng, T.Cheng, J.Li, Y.Yin, X.Zeng, W.Jin, X.Li, Y.Guo, F.Jin, T.

(2017) Biochem. Biophys. Res. Commun. 492: 624-630

  • DOI: 10.1016/j.bbrc.2016.11.098
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recent outbreak of flavivirus Zika virus (ZIKV) in America has urged the basic as well as translational studies of this important human pathogen. The nonstructural protein 5 (NS5) of the flavivirus has an N-terminal methyltransferase (MTase) domain t ...

    Recent outbreak of flavivirus Zika virus (ZIKV) in America has urged the basic as well as translational studies of this important human pathogen. The nonstructural protein 5 (NS5) of the flavivirus has an N-terminal methyltransferase (MTase) domain that plays critical roles in viral RNA genome capping. The null mutant of NS5 MTase is lethal for virus. Therefore, NS5 is a potential drug target for the treatment of Zika virus infection. In this study, we determined crystal structures of the ZIKV MTase in complex with GTP and RNA cap analogue 7me GpppA. Structural analyses revealed highly conserved GTP/cap-binding pocket and S-adenosylmethionine (SAM)-binding pocket. Two conformations of the second base of the cap were identified, which suggests the flexibility of RNA conformation. In addition, the ligand-binding pockets identified a continuous region of hotspots suitable for drug design. Docking calculation shows that the Dengue virus inhibitor compound 10 may bind to the ZIKV MTase.


    Organizational Affiliation

    Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, 230027, China.,Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, 230027, China. Electronic address: jint@ustc.edu.cn.,School of Medicine, Stanford University, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase NS5
A, B, C
269Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)Mutation(s): 0 
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Go to UniProtKB:  A0A024B7W1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B, C
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
GTA
Query on GTA

Download SDF File 
Download CCD File 
A, B, C
P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE
7-METHYL-GPPPA
C21 H30 N10 O17 P3
QQOHNVHGNZYSBP-XPWFQUROSA-O
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.444 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 123.770α = 90.00
b = 123.770β = 90.00
c = 119.360γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-07-30 
  • Released Date: 2016-12-07 
  • Deposition Author(s): Zhang, C., Jin, T.

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references