5NEQ

The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with aminoguanidine

• PDB DOI: https://doi.org/10.2210/pdb5NEQ/pdb
• NAKB: 5NEQ

• Classification: RNA
• Organism(s): Gloeobacter violaceus
• Mutation(s): No 


• Deposited: 2017-03-11 Released: 2017-05-31 
• Deposition Author(s): Huang, L., Wang, J., Lilley, D.M.J.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.252 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

The Structure of the Guanidine-II Riboswitch.

Huang, L., Wang, J., Lilley, D.M.J.

(2017) Cell Chem Biol 24: 695-702.e2

• PubMed: 28529131 
• DOI: https://doi.org/10.1016/j.chembiol.2017.05.014
• Primary Citation of Related Structures:  
  5NDH, 5NDI, 5NEF, 5NEO, 5NEP, 5NEQ, 5NEX, 5NOM


• PubMed Abstract: 
  

  The guanidine-II (mini-ykkC) riboswitch is the smallest of the guanidine-responsive riboswitches, comprising two stem loops of similar sequence. We have solved high-resolution crystal structures of both stem loops for the riboswitch from Gloeobacter violaceus. The stem loops have a strong propensity to dimerize by intimate loop-loop interaction. The dimerization creates specific binding pockets for two guanidine molecules, explaining their cooperative binding. Within the binding pockets the ligands are hydrogen bonded to a guanine at O6 and N7, and to successive backbone phosphates. Additionally they are each stacked upon a guanine nucleobase. One side of the pocket has an opening to the solvent, slightly lowering the specificity of ligand binding, and structures with bound methylguanidine, aminoguanidine, and agmatine show how this is possible.

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Organizational Affiliation: 

Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.31 kDa 
• Atom Count: 443 
• Modelled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')	A	18	Gloeobacter violaceus

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
AGU	B [auth A]	AMINOGUANIDINE C H6 N4 HAMNKKUPIHEESI-UHFFFAOYSA-N
NA	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.252 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.463	α = 90
b = 55.463	β = 90
c = 130.276	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Huang, L., Wang, J., Lilley, D.M.J.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	--

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Database references
• Version 1.2: 2017-08-30
  Changes: Author supporting evidence
• Version 1.3: 2019-03-20
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2019-07-10
  Changes: Data collection
• Version 1.5: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description