5Y6N

Zika virus helicase in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Mechanism of ATP hydrolysis by the Zika virus helicase.

Yang, X.Chen, C.Tian, H.Chi, H.Mu, Z.Zhang, T.Yang, K.Zhao, Q.Liu, X.Wang, Z.Ji, X.Yang, H.

(2018) FASEB J 32: 5250-5257

  • DOI: https://doi.org/10.1096/fj.201701140R
  • Primary Citation of Related Structures:  
    5Y6M, 5Y6N

  • PubMed Abstract: 

    During its life cycle, Zika virus (ZIKV), an arthropod-borne flavivirus that is associated with Guillain-Barré syndrome and causes microencephaly in fetuses and newborn children, encodes a critical and indispensable helicase domain that has 5'-triphosphatase activity and performs ATP hydrolysis to generate energy and thus, sustains unwinding of double-stranded RNA during ZIKV genome replication. Of these processes, ATP hydrolysis represents the most basic event; however, its dynamic mechanisms remain largely unknown, impeding the further understanding of the function of ZIKV helicase and the ongoing anti-ZIKV drug design. In this work, we determined the crystal structure of ZIKV helicase in complex with ADP-AlF 3 -Mn 2+ and ADP-Mn 2+ separately. The structural analysis indicates that these structures represent the intermediate state and posthydrolysis state, respectively, of the ATP hydrolysis process of ZIKV helicase. These findings, together with our earlier work, which identified the prehydrolysis state of ZIKV helicase, lead to a proposal of the ATP hydrolysis cycle for ZIKV helicase. On this basis, we used site-directed mutagenesis combined with an enzymatic study to identify successfully residues that are critical for the ATPase activity of ZIKV helicase; this will provide new ideas to understand the function for the key enzyme of ZIKV.-Yang, X., Chen, C., Tian, H., Chi, H., Mu, Z., Zhang, T., Yang, K., Zhao, Q., Liu, X., Wang, Z., Ji, X., Yang, H. Mechanism of ATP hydrolysis by the Zika virus helicase.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Helicase domain from Genome polyprotein438Zika virusMutation(s): 0 
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Explore A0A024B7W1 
Go to UniProtKB:  A0A024B7W1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024B7W1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.275α = 90
b = 52.934β = 104.93
c = 64.483γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ChinaNos. 2015CB859800 and 2014CB542800
National Natural Science Foundation of ChinaChinaGrant Nos. 31528006
ChinaNo. 2016YFD0500300

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description