4P97

Functional conservation despite structural divergence in ligand-responsive RNA switches


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.212 

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.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 (5'-R(*CP*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*C)-3')A,C16Senecavirus A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*GP*AP*GP*AP*GP*GP*AP*CP*GP*G)-3')B,D11Senecavirus A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.212 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 60.532α = 90.00
b = 60.532β = 90.00
c = 122.679γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

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 Allergy and Infectious DiseasesUnited StatesR01AI072012

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Source and taxonomy