Crystal structure of xanthine riboswitch with xanthine, iridium hexammine soak

Experimental Data Snapshot

  • Resolution: 2.79 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

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Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition.

Xu, X.Egger, M.Chen, H.Bartosik, K.Micura, R.Ren, A.

(2021) Nucleic Acids Res 49: 7139-7153

  • DOI: https://doi.org/10.1093/nar/gkab486
  • Primary Citation of Related Structures:  
    7ELP, 7ELQ, 7ELR, 7ELS

  • PubMed Abstract: 

    Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson-Crick base pair to junction J2. Xanthine inserts between a G-U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.

  • Organizational Affiliation

    Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.

Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
A, B
45Ideonella sp. B508-1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GTP

Download Ideal Coordinates CCD File 
C [auth A],
S [auth B]
C10 H16 N5 O14 P3
IR (Subject of Investigation/LOI)
Query on IR

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
T [auth B]
XAN (Subject of Investigation/LOI)
Query on XAN

Download Ideal Coordinates CCD File 
F [auth A],
U [auth B]
C5 H4 N4 O2
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.79 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.465α = 90
b = 100.192β = 90
c = 40.267γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references