3VRS: Crystal Structure Of Fluoride Riboswitch, Soaked In Mn2+

Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure-function studies on riboswitches, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoogsteen A*U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg(2+) ions, which in turn are octahedrally coordinated to water molecules and five inwardly pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state shows how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch probably functions in gene regulation through a transcription termination mechanism.
PDB ID: 3VRSDownload
MMDB ID: 99390
PDB Deposition Date: 2012/4/13
Updated in MMDB: 2012/06
Experimental Method:
x-ray diffraction
Resolution: 2.6  Å
Source Organism:
Biological Unit for 3VRS: monomeric; determined by author and by software (PISA)
Molecular Components in 3VRS
Label Count Molecule
Nucleotide(1 molecule)
Fluoride Riboswitch
Molecule annotation
Chemicals (11 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB