4PHY

Functional conservation despite structural divergence in ligand-responsive RNA switches


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 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.USA 111: 15952-15957

  • DOI: 10.1073/pnas.1414678111
  • Primary Citation of Related Structures:  

  • 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 sequ ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (26-MER)A26Senecavirus A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*CP*AP*GP*GP*AP*AP*CP*CP*GP*AP*GP*AP*GP*GP*CP*AP*CP*GP*C)-3')B20Senecavirus A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.215 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.611α = 90.00
b = 79.611β = 90.00
c = 100.940γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release