6D3P

Crystal structure of an exoribonuclease-resistant RNA from Sweet clover necrotic mosaic virus (SCNMV)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure.

Steckelberg, A.L.Akiyama, B.M.Costantino, D.A.Sit, T.L.Nix, J.C.Kieft, J.S.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 6404-6409

  • DOI: 10.1073/pnas.1802429115

  • PubMed Abstract: 
  • Folded RNA elements that block processive 5' → 3' cellular exoribonucleases (xrRNAs) to produce biologically active viral noncoding RNAs have been discovered in flaviviruses, potentially revealing a new mode of RNA maturation. However, whether this R ...

    Folded RNA elements that block processive 5' → 3' cellular exoribonucleases (xrRNAs) to produce biologically active viral noncoding RNAs have been discovered in flaviviruses, potentially revealing a new mode of RNA maturation. However, whether this RNA structure-dependent mechanism exists elsewhere and, if so, whether a singular RNA fold is required, have been unclear. Here we demonstrate the existence of authentic RNA structure-dependent xrRNAs in dianthoviruses, plant-infecting viruses unrelated to animal-infecting flaviviruses. These xrRNAs have no sequence similarity to known xrRNAs; thus, we used a combination of biochemistry and virology to characterize their sequence requirements and mechanism of stopping exoribonucleases. By solving the structure of a dianthovirus xrRNA by X-ray crystallography, we reveal a complex fold that is very different from that of the flavivirus xrRNAs. However, both versions of xrRNAs contain a unique topological feature, a pseudoknot that creates a protective ring around the 5' end of the RNA structure; this may be a defining structural feature of xrRNAs. Single-molecule FRET experiments reveal that the dianthovirus xrRNAs undergo conformational changes and can use "codegradational remodeling," exploiting the exoribonucleases' degradation-linked helicase activity to help form their resistant structure; such a mechanism has not previously been reported. Convergent evolution has created RNA structure-dependent exoribonuclease resistance in different contexts, which establishes it as a general RNA maturation mechanism and defines xrRNAs as an authentic functional class of RNAs.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (45-MER)A45Sweet clover necrotic mosaic virus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IRI
Query on IRI

Download SDF File 
Download CCD File 
A
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.241 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 83.400α = 90.00
b = 83.400β = 90.00
c = 94.210γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
AutoSolphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35GM118070
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI133348
European Molecular Biology OrganizationGermanyALTF 611-2015
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF32GM117730
National Institutes of Health/National Cancer InstituteUnited StatesP30CA046934

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-07-04
    Type: Data collection, Database references