5TPY

Crystal structure of an exonuclease resistant RNA from Zika virus

• PDB DOI: https://doi.org/10.2210/pdb5TPY/pdb
• NAKB: 5TPY

• Classification: RNA
• Organism(s): Zika virus
• Mutation(s): No 


• Deposited: 2016-10-21 Released: 2016-12-14 
• Deposition Author(s): 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.

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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 

Starting Model: experimental

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

• PubMed: 27934765 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.16 kDa 
• Atom Count: 1,546 
• Modelled Residue Count: 71 
• Deposited Residue Count: 71 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (71-MER)	A	71	Zika virus

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEZ	C [auth A]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 111.679	α = 90
b = 111.679	β = 90
c = 90.826	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2017-01-04
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description