5T83 | pdb_00005t83

Structure of a guanidine-I riboswitch from S. acidophilus

• PDB DOI: https://doi.org/10.2210/pdb5T83/pdb
• NAKB: 5T83

• Classification: RNA
• Organism(s): Sulfobacillus acidophilus DSM 10332
• Mutation(s): Yes 


• Deposited: 2016-09-06 Released: 2017-01-11 
• Deposition Author(s): Reiss, C.W., Xiong, Y., Strobel, S.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Structural Basis for Ligand Binding to the Guanidine-I Riboswitch.

Reiss, C.W., Xiong, Y., Strobel, S.A.

(2017) Structure 25: 195-202

• PubMed: 28017522 
• DOI: https://doi.org/10.1016/j.str.2016.11.020
• Primary Citation Related Structures: 
  5T83


• PubMed Abstract: 
  

  The guanidine-I riboswitch is a conserved RNA element with approximately 2,000 known examples across four phyla of bacteria. It exists upstream of nitrogen metabolism and multidrug resistance transporter genes and alters expression through the specific recognition of a free guanidinium cation. Here we report the structure of a guanidine riboswitch aptamer from Sulfobacillus acidophilus at 2.7 Å resolution. Helices P1, P1a, P1b, and P2 form a coaxial stack that acts as a scaffold for ligand binding. A previously unidentified P3 helix docks into P1a to form the guanidinium binding pocket, which is completely enclosed. Every functional group of the ligand is recognized through hydrogen bonding to guanine bases and phosphate oxygens. Guanidinium binding is further stabilized through cation-π interactions with guanine bases. This allows the riboswitch to recognize guanidinium while excluding other bacterial metabolites with a guanidino group, including the amino acid arginine.

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Organizational Affiliation: 
• Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.
Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA.
Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 32.72 kDa 
• Atom Count: 1,985 
• Modeled Residue Count: 90 
• Deposited Residue Count: 95 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (95-MER)	A	95	Sulfobacillus acidophilus DSM 10332

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IRI	N [auth A], O [auth A], P [auth A]	IRIDIUM HEXAMMINE ION H18 Ir N6 CGMAOQLDNKCXGK-UHFFFAOYSA-N
SPK	K [auth A]	SPERMINE (FULLY PROTONATED FORM) C10 H30 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-R
SR	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]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N
GAI	Q [auth A]	GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N
MG	L [auth A], M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.091	α = 90
b = 49.091	β = 90
c = 246.341	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Reiss, C.W., Xiong, Y., Strobel, S.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM022778

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Refinement description
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations