Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO

Experimental Data Snapshot

  • Resolution: 3.12 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.236 

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Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA.

Jones, C.P.Ferre-D'Amare, A.R.

(2014) EMBO J 33: 2692-2703

  • DOI: https://doi.org/10.15252/embj.201489209
  • Primary Citation of Related Structures:  
    4W90, 4W92

  • PubMed Abstract: 

    Cyclic diadenosine monophosphate (c-di-AMP) is a second messenger that is essential for growth and homeostasis in bacteria. A recently discovered c-di-AMP-responsive riboswitch controls the expression of genes in a variety of bacteria, including important pathogens. To elucidate the molecular basis for specific binding of c-di-AMP by a gene-regulatory mRNA domain, we have determined the co-crystal structure of this riboswitch. Unexpectedly, the structure reveals an internally pseudo-symmetric RNA in which two similar three-helix-junction elements associate head-to-tail, creating a trough that cradles two c-di-AMP molecules making quasi-equivalent contacts with the riboswitch. The riboswitch selectively binds c-di-AMP and discriminates exquisitely against other cyclic dinucleotides, such as c-di-GMP and cyclic-AMP-GMP, via interactions with both the backbone and bases of its cognate second messenger. Small-angle X-ray scattering experiments indicate that global folding of the riboswitch is induced by the two bound cyclic dinucleotides, which bridge the two symmetric three-helix domains. This structural reorganization likely couples c-di-AMP binding to gene expression.

  • Organizational Affiliation

    Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA adrian.ferre@nih.gov.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein AA [auth B]91Homo sapiensMutation(s): 2 
Gene Names: U1A proteinSNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09012
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
riboswitch a pseudo-dimeric RNAB [auth C]119Bacillus subtilis
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 3.12 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.236 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.28α = 90
b = 84.85β = 90
c = 230.536γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-12-03
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy