5U04 | pdb_00005u04

Crystal structure of Zika virus NS5 RNA-dependent RNA polymerase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.207 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.7 of the entry. See complete history. 

Literature

Crystal structure of Zika virus NS5 RNA-dependent RNA polymerase.

Godoy, A.S., Lima, G.M., Oliveira, K.I., Torres, N.U., Maluf, F.V., Guido, R.V., Oliva, G.

(2017) Nat Commun 8: 14764-14764

  • DOI: https://doi.org/10.1038/ncomms14764
  • Primary Citation Related Structures: 
    5U04

  • PubMed Abstract: 

    The current Zika virus (ZIKV) outbreak became a global health threat of complex epidemiology and devastating neurological impacts, therefore requiring urgent efforts towards the development of novel efficacious and safe antiviral drugs. Due to its central role in RNA viral replication, the non-structural protein 5 (NS5) RNA-dependent RNA-polymerase (RdRp) is a prime target for drug discovery. Here we describe the crystal structure of the recombinant ZIKV NS5 RdRp domain at 1.9 Å resolution as a platform for structure-based drug design strategy. The overall structure is similar to other flaviviral homologues. However, the priming loop target site, which is suitable for non-nucleoside polymerase inhibitor design, shows significant differences in comparison with the dengue virus structures, including a tighter pocket and a modified local charge distribution.

    • Organizational Affiliation: 
    • Institute of Physics of São Carlos, University of São Paulo, Av. Joao Dagnone, 1100-Jardim Santa Angelina, São Carlos 13563-120, Brazil.

Macromolecule Content 

  • Total Structure Weight: 69.25 kDa 
  • Atom Count: 4,548 
  • Modeled Residue Count: 478 
  • Deposited Residue Count: 598 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zika Virus NS5 RdRp598Zika virusMutation(s): 0 
UniProt
Find proteins for Q32ZE1 (Zika virus)
Explore Q32ZE1 
Go to UniProtKB:  Q32ZE1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ32ZE1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.207 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.954α = 90
b = 78.954β = 90
c = 210.022γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2013/07600-3

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Structure summary
  • Version 1.2: 2017-04-05
    Changes: Database references
  • Version 1.3: 2017-04-12
    Changes: Database references
  • Version 1.4: 2017-04-26
    Changes: Data collection
  • Version 1.5: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.6: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.7: 2023-10-04
    Changes: Data collection, Database references, Refinement description