4ENC

Crystal structure of fluoride riboswitch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.272 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch.

Ren, A.Rajashankar, K.R.Patel, D.J.

(2012) Nature 486: 85-89

  • DOI: 10.1038/nature11152
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 cont ...

    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.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Center, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Fluoride riboswitchA52Thermotoga petrophila
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
F
Query on F

Download SDF File 
Download CCD File 
A
FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.272 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.010α = 90.00
b = 75.223β = 90.00
c = 42.905γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXmodel building
HKL-2000data reduction
ADSCdata collection
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2012-06-20
    Type: Database references
  • Version 1.2: 2013-02-13
    Type: Structure summary