9UW0 | pdb_00009uw0

Crystal structure of 2'-dG-III riboswitch with Guanosine, manganese saok


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.223 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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Literature

Structure-based insights into the ligand specificity tuning of 2'-dG-III riboswitch.

Shen, X.Li, H.Xu, X.Song, Q.Tai, X.He, M.Ren, A.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf773
  • Primary Citation of Related Structures:  
    9LKU, 9LKV, 9LKW, 9UW0

  • PubMed Abstract: 

    Riboswitches are conserved non-coding RNA domains predominantly located at the 5'-end of the bacterial mRNAs, serving as gene expression regulators. Recently, a third class of 2'-deoxyguanosine riboswitch (2'-dG-III) has been identified from guanine riboswitch family, exhibiting comparable binding affinity toward 2'-dG, guanine, and guanosine. To elucidate the unique ligand recognition mechanism of this riboswitch, we solved its crystal structures in complex with different purine derivatives, including 2'-dG, guanine, and guanosine. The tertiary structure reveals a typical tuning-fork-like architecture, with three stems converging at a central three-way junction. The bound ligand, 2'-dG, is anchored within the junctional core through specific molecular interactions involving certain critical nucleotides. Through systemic comparative analysis of the binding pocket across different ligand-bound states, as well as related guanine family riboswitches, including 2'-dG-I, 2'-dG-II, and Guanine-I riboswitches, we identified subtle yet significant structural variations that modulate binding affinity and specificity. Leveraging these findings, we further engineered RNA biosensors by fusing the 2'-dG-III riboswitch with Pepper fluorogenic RNA aptamer, which exhibits a robust, positive correlation between fluorescence intensity and 2'-dG levels in vitro. Together, this work not only advances our understanding of the ligand recognition mechanisms underlying the 2'-dG-III riboswitch and related guanine riboswitch family but also lays the groundwork for fine-tuning riboswitch specificity, paving the way for the development of highly specific RNA-based biosensors.


  • Organizational Affiliation
    • Department of Cardiology of The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, Zhejiang University, Hangzhou 310058, China.

Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (65-MER)A [auth X]65synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GMP (Subject of Investigation/LOI)
Query on GMP

Download Ideal Coordinates CCD File 
B [auth X]GUANOSINE
C10 H13 N5 O5
NYHBQMYGNKIUIF-UUOKFMHZSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth X]
D [auth X]
E [auth X]
F [auth X]
G [auth X]
C [auth X],
D [auth X],
E [auth X],
F [auth X],
G [auth X],
H [auth X]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth X]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.223 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.206α = 90
b = 70.365β = 90
c = 116.266γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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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: 2025-08-20
    Type: Initial release