5TPY

Crystal structure of an exonuclease resistant RNA from Zika virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.805 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease.

Akiyama, B.M.Laurence, H.M.Massey, A.R.Costantino, D.A.Xie, X.Yang, Y.Shi, P.Y.Nix, J.C.Beckham, J.D.Kieft, J.S.

(2016) Science 354: 1148-1152

  • DOI: 10.1126/science.aah3963

  • PubMed Abstract: 
  • The outbreak of Zika virus (ZIKV) and associated fetal microcephaly mandates efforts to understand the molecular processes of infection. Related flaviviruses produce noncoding subgenomic flaviviral RNAs (sfRNAs) that are linked to pathogenicity in fe ...

    The outbreak of Zika virus (ZIKV) and associated fetal microcephaly mandates efforts to understand the molecular processes of infection. Related flaviviruses produce noncoding subgenomic flaviviral RNAs (sfRNAs) that are linked to pathogenicity in fetal mice. These viruses make sfRNAs by co-opting a cellular exonuclease via structured RNAs called xrRNAs. We found that ZIKV-infected monkey and human epithelial cells, mouse neurons, and mosquito cells produce sfRNAs. The RNA structure that is responsible for ZIKV sfRNA production forms a complex fold that is likely found in many pathogenic flaviviruses. Mutations that disrupt the structure affect exonuclease resistance in vitro and sfRNA formation during infection. The complete ZIKV xrRNA structure clarifies the mechanism of exonuclease resistance and identifies features that may modulate function in diverse flaviviruses.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (71-MER)A71Zika virus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

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Download CCD File 
A
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.805 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 111.679α = 90.00
b = 111.679β = 90.00
c = 90.826γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-01-04
    Type: Database references