5GJB | pdb_00005gjb

Zika virus NS3 helicase in complex with ssRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.196 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.154 (Depositor) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5GJB

This is version 1.3 of the entry. See complete history

Literature

Structural basis of Zika virus helicase in recognizing its substrates

Tian, H.L.Ji, X.Y.Yang, X.Y.Zhang, Z.X.Lu, Z.K.Yang, K.L.Chen, C.Zhao, Q.Chi, H.Mu, Z.Y.Xie, W.Wang, Z.F.Lou, H.Q.Yang, H.T.Rao, Z.H.

(2016) Protein Cell 7: 562-570

  • DOI: https://doi.org/10.1007/s13238-016-0293-2
  • Primary Citation Related Structures: 
    5GJB, 5GJC

  • PubMed Abstract: 

    The recent explosive outbreak of Zika virus (ZIKV) infection has been reported in South and Central America and the Caribbean. Neonatal microcephaly associated with ZIKV infection has already caused a public health emergency of international concern. No specific vaccines or drugs are currently available to treat ZIKV infection. The ZIKV helicase, which plays a pivotal role in viral RNA replication, is an attractive target for therapy. We determined the crystal structures of ZIKV helicase-ATP-Mn(2+) and ZIKV helicase-RNA. This is the first structure of any flavivirus helicase bound to ATP. Comparisons with related flavivirus helicases have shown that although the critical P-loop in the active site has variable conformations among different species, it adopts an identical mode to recognize ATP/Mn(2+). The structure of ZIKV helicase-RNA has revealed that upon RNA binding, rotations of the motor domains can cause significant conformational changes. Strikingly, although ZIKV and dengue virus (DENV) apo-helicases share conserved residues for RNA binding, their different manners of motor domain rotations result in distinct individual modes for RNA recognition. It suggests that flavivirus helicases could have evolved a conserved engine to convert chemical energy from nucleoside triphosphate to mechanical energy for RNA unwinding, but different motor domain rotations result in variable RNA recognition modes to adapt to individual viral replication.


  • Organizational Affiliation
    • School of Life Sciences, Tianjin University, Tianjin, 300072, China.

Macromolecule Content 

  • Total Structure Weight: 52.8 kDa 
  • Atom Count: 4,132 
  • Modeled Residue Count: 445 
  • Deposited Residue Count: 457 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NS3 helicase450Zika virusMutation(s): 0 
UniProt
Find proteins for A0A0U4DG08 (Zika virus)
Explore A0A0U4DG08 
Go to UniProtKB:  A0A0U4DG08
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U4DG08
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*AP*GP*AP*UP*CP*AP*A)-3')7synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.196 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.154 (Depositor) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.316α = 90
b = 72.252β = 94.45
c = 59.409γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2016-08-31
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description