4P97

Functional conservation despite structural divergence in ligand-responsive RNA switches

  • Classification: RNA
  • Organism(s): Senecavirus A
  • Mutation(s): No 

  • Deposited: 2014-04-02 Released: 2015-03-04 
  • Deposition Author(s): Boerneke, M.A., Dibrov, S.M., Hermann, T.H.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 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

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*C)-3')
A, C
16Senecavirus A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*GP*AP*GP*AP*GP*GP*AP*CP*GP*G)-3')
B, D
11Senecavirus A
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.532α = 90
b = 60.532β = 90
c = 122.679γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI072012

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations