4PHY

Functional conservation despite structural divergence in ligand-responsive RNA switches

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.268 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Functional conservation despite structural divergence in ligand-responsive RNA switches.

Boerneke, M.A., Dibrov, S.M., Gu, J., Wyles, D.L., Hermann, T.

(2014) Proc Natl Acad Sci U S A 111: 15952-15957

  • DOI: https://doi.org/10.1073/pnas.1414678111
  • Primary Citation of Related Structures:  
    4P97, 4PHY

  • PubMed Abstract: 

    An internal ribosome entry site (IRES) initiates protein synthesis in RNA viruses, including the hepatitis C virus (HCV). We have discovered ligand-responsive conformational switches in viral IRES elements. Modular RNA motifs of greatly distinct sequence and local secondary structure have been found to serve as functionally conserved switches involved in viral IRES-driven translation and may be captured by identical cognate ligands. The RNA motifs described here constitute a new paradigm for ligand-captured switches that differ from metabolite-sensing riboswitches with regard to their small size, as well as the intrinsic stability and structural definition of the constitutive conformational states. These viral RNA modules represent the simplest form of ligand-responsive mechanical switches in nucleic acids.

    • Organizational Affiliation: 

    Department of Chemistry and Biochemistry.


Macromolecules
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (26-MER)26Senecavirus A
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*CP*AP*GP*GP*AP*AP*CP*CP*GP*AP*GP*AP*GP*GP*CP*AP*CP*GP*C)-3')20Senecavirus A
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.268 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.611α = 90
b = 79.611β = 90
c = 100.94γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy