5TPY

Crystal structure of an exonuclease resistant RNA from Zika virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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
  • Primary Citation of Related Structures:  
    5TPY

  • 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 fetal mice ...

    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

    RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (71-MER)A71Zika virus
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
C [auth A]HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.679α = 90
b = 111.679β = 90
c = 90.826γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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