6MJ0

Crystal structure of the complete turnip yellow mosaic virus 3'UTR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels.

Hartwick, E.W.Costantino, D.A.MacFadden, A.Nix, J.C.Tian, S.Das, R.Kieft, J.S.

(2018) Nat Commun 9: 5074-5074

  • DOI: https://doi.org/10.1038/s41467-018-07542-x
  • Primary Citation of Related Structures:  
    6MJ0

  • PubMed Abstract: 

    Structured RNA elements, programmed RNA conformational changes, and interactions between different RNA domains underlie many modes of regulating gene expression, mandating studies to understand the foundational principles that govern these phenomena. Exploring the structured 3' untranslated region (UTR) of a viral RNA, we discovered that different contexts of the 3'-UTR confer different abilities to enhance translation of an associated open reading frame. In one context, ribosome-induced conformational changes in a 'sensor' RNA domain affect a separate RNA 'functional' domain, altering translation efficiency. The structure of the entire 3'-UTR reveals that structurally distinct domains use a spine of continuously stacked bases and a strut-like linker to create a conduit for communication within the higher-order architecture. Thus, this 3'-UTR RNA illustrates how RNA can use programmed conformational changes to sense the translation status of an upstream open reading frame, then create a tuned functional response by communicating that information to other RNA elements.


  • Organizational Affiliation

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


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (101-MER)
A, B
104Turnip yellow mosaic virus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.032α = 90
b = 129.126β = 90
c = 172.005γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR35GM118070
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM097333
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesP30CA046934
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesS10OD012033
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description