5WXB

crystal structure of ZIKV MTase in complex with SAH

• PDB DOI: https://doi.org/10.2210/pdb5WXB/pdb

• Classification: TRANSFERASE
• Organism(s): Zika virus
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-01-07 Released: 2017-05-17 
• Deposition Author(s): Yang, H., Wang, L., Zhou, H.
• Funding Organization(s): National Basic Research program, National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.199 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

The conformational changes of Zika virus methyltransferase upon converting SAM to SAH

Zhou, H., Wang, F., Wang, H., Chen, C., Zhang, T., Han, X., Wang, D., Chen, C., Wu, C., Xie, W., Wang, Z., Zhang, L., Wang, L., Yang, H.

(2017) Oncotarget 8: 14830-14834

• PubMed: 28122329 
• DOI: https://doi.org/10.18632/oncotarget.14780
• Primary Citation of Related Structures:  
  5WXB


• PubMed Abstract: 
  

  An outbreak of Zika virus (ZIKV) infection has been reported in South and Central America and the Caribbean. Neonatal microcephaly potentially associated with ZIKV infection has already caused a public health emergency of international concern. Currently, there are no clinically effective vaccines or antiviral drugs available to treat ZIKV infection. The methyltransferase domain (MTase) of ZIKV nonstructural protein 5 (NS5) can sequentially methylate guanine N-7 and ribose 2'-O to form m7NGpppA2'Om cap structure in the new RNA transcripts. This methylation step is crucial for ZIKV replication cycle and evading the host immune system, making it a target for drug design. Here, we present the 1.76 Å crystal structure of ZIKV MTase in complex with the byproduct SAH, providing insight into the elegant methylation process, which will benefit the following antiviral drug development.

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Organizational Affiliation: 

School of Life Sciences, Tianjin University, Tianjin 300072, China.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 29.75 kDa 
• Atom Count: 2,407 
• Modelled Residue Count: 264 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MRNA cap 0-1 NS5-type MT	A	266	Zika virus	Mutation(s): 0  Gene Names: GP1, A2G93_63486gpGP1
UniProt
Find proteins for A0A167V0D5 (Zika virus) Explore A0A167V0D5  Go to UniProtKB:  A0A167V0D5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.199 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.991	α = 90
b = 76.862	β = 90
c = 109.582	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-17 
Deposition Author(s): Yang, H., Wang, L., Zhou, H.

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Funding Organization	Location	Grant Number
National Basic Research program	China	2015CB859800
National Natural Science Foundation of China	China	No. 31528006

Revision History  

• Version 1.0: 2017-05-17
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary