4P5J

Crystal structure of the tRNA-like structure from Turnip Yellow Mosaic Virus (TYMV), a tRNA mimicking RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9912 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA.

Colussi, T.M.Costantino, D.A.Hammond, J.A.Ruehle, G.M.Nix, J.C.Kieft, J.S.

(2014) Nature 511: 366-369

  • DOI: 10.1038/nature13378

  • PubMed Abstract: 
  • RNA is arguably the most functionally diverse biological macromolecule. In some cases a single discrete RNA sequence performs multiple roles, and this can be conferred by a complex three-dimensional structure. Such multifunctionality can also be driv ...

    RNA is arguably the most functionally diverse biological macromolecule. In some cases a single discrete RNA sequence performs multiple roles, and this can be conferred by a complex three-dimensional structure. Such multifunctionality can also be driven or enhanced by the ability of a given RNA to assume different conformational (and therefore functional) states. Despite its biological importance, a detailed structural understanding of the paradigm of RNA structure-driven multifunctionality is lacking. To address this gap it is useful to study examples from single-stranded positive-sense RNA viruses, a prototype being the tRNA-like structure (TLS) found at the 3' end of the turnip yellow mosaic virus (TYMV). This TLS not only acts like a tRNA to drive aminoacylation of the viral genomic (g)RNA, but also interacts with other structures in the 3' untranslated region of the gRNA, contains the promoter for negative-strand synthesis, and influences several infection-critical processes. TLS RNA can provide a glimpse into the structural basis of RNA multifunctionality and plasticity, but for decades its high-resolution structure has remained elusive. Here we present the crystal structure of the complete TYMV TLS to 2.0 Å resolution. Globally, the RNA adopts a shape that mimics tRNA, but it uses a very different set of intramolecular interactions to achieve this shape. These interactions also allow the TLS to readily switch conformations. In addition, the TLS structure is 'two faced': one face closely mimics tRNA and drives aminoacylation, the other face diverges from tRNA and enables additional functionality. The TLS is thus structured to perform several functions and interact with diverse binding partners, and we demonstrate its ability to specifically bind to ribosomes.


    Related Citations: 
    • Comparison and functional implications of the 3D architectures of viral tRNA-like structures.
      Hammond, J.A.,Rambo, R.P.,Filbin, M.E.,Kieft, J.S.
      (2009) Rna 15: 294
    • Multi-domain packing in the aminoacylatable 3' end of a plant viral RNA.
      Hammond, J.A.,Rambo, R.P.,Kieft, J.S.
      (2010) J.Mol.Biol. 399: 450


    Organizational Affiliation

    1] Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA [2] Howard Hughes Medical Institute, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA [3] Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA (T.M.C.); Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037, USA (J.A.H.).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Turnip yellow mosaic virus mRNA for the coat proteinA86Turnip yellow mosaic virus
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download SDF File 
Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IRI
Query on IRI

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Download CCD File 
A
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
A23
Query on A23
A
RNA LINKINGC10 H13 N5 O9 P2A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9912 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 55.270α = 90.00
b = 101.570β = 90.00
c = 111.610γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--
National Institutes of Health/National Cancer InstituteUnited StatesP30CA046934
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM081346
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM097333
Department of Energy (United States)United StatesDE-AC02-05CH11231

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-06-25
    Type: Database references
  • Version 1.2: 2014-07-30
    Type: Database references
  • Version 1.3: 2014-10-01
    Type: Database references
  • Version 1.4: 2017-09-06
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy