5O69

The structure of the thermobifida fusca guanidine III riboswitch with agmatine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.319 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the Guanidine III Riboswitch.

Huang, L.Wang, J.Wilson, T.J.Lilley, D.M.J.

(2017) Cell Chem Biol 24: 1407-1415.e2

  • DOI: 10.1016/j.chembiol.2017.08.021
  • Primary Citation of Related Structures:  5NWQ, 5NY8, 5NZ3, 5NZ6, 5NZD, 5O62

  • PubMed Abstract: 
  • Riboswitches are structural elements found in mRNA molecules that couple small-molecule binding to regulation of gene expression, usually by controlling transcription or translation. We have determined high-resolution crystal structures of the ykkC g ...

    Riboswitches are structural elements found in mRNA molecules that couple small-molecule binding to regulation of gene expression, usually by controlling transcription or translation. We have determined high-resolution crystal structures of the ykkC guanidine III riboswitch from Thermobifida fusca. The riboswitch forms a classic H-type pseudoknot that includes a triple helix that is continuous with a central core of conserved nucleotides. These form a left-handed helical ramp of inter-nucleotide interactions, generating the guanidinium cation binding site. The ligand is hydrogen bonded to the Hoogsteen edges of two guanine bases. The binding pocket has a side opening that can accommodate a small side chain, shown by structures with bound methylguanidine, aminoguanidine, ethylguanidine, and agmatine. Comparison of the new structure with those of the guanidine I and II riboswitches reveals that evolution generated three different structural solutions for guanidine binding and subsequent gene regulation, although with some common elements.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (41-MER)A41Thermobifida fusca
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (37-MER)B41Thermobifida fusca
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AG2
Query on AG2

Download SDF File 
Download CCD File 
A
AGMATINE
(4-AMINOBUTYL)GUANIDINE
C5 H14 N4
QYPPJABKJHAVHS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CBV
Query on CBV
A, B
RNA LINKINGC9 H13 Br N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.319 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.243 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.886α = 90.00
b = 83.886β = 90.00
c = 67.226γ = 120.00
Software Package:
Software NamePurpose
xia2data scaling
PHENIXphasing
xia2data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Cancer Research UKUnited Kingdomprogram grant A18604

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-11-29
    Type: Database references