3VRS | pdb_00003vrs

Crystal structure of fluoride riboswitch, soaked in Mn2+

• PDB DOI: https://doi.org/10.2210/pdb3VRS/pdb
• NAKB: 3VRS

• Classification: RNA
• Organism(s): Thermotoga petrophila
• Mutation(s): No 


• Deposited: 2012-04-13 Released: 2012-05-09 
• Deposition Author(s): Ren, A.M., Rajashankar, K.R., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.262 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

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

• PubMed: 22678284 
• DOI: https://doi.org/10.1038/nature11152
• Primary Citation Related Structures: 
  3VRS, 4EN5, 4ENA, 4ENB, 4ENC


• 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 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.

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Organizational Affiliation: 
• Structural Biology Program, Memorial Sloan-Kettering Center, New York, New York 10065, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.33 kDa 
• Atom Count: 1,139 
• Modeled Residue Count: 52 
• Deposited Residue Count: 52 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Fluoride riboswitch	A	52	Thermotoga petrophila

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
K	K [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
F	L [auth A]	FLUORIDE ION F KRHYYFGTRYWZRS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.262 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.846	α = 90
b = 77.203	β = 90
c = 42.094	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Ren, A.M., Rajashankar, K.R., Patel, D.J.

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2012-06-20
  Changes: Database references
• Version 1.2: 2013-02-13
  Changes: Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description