7OAX

Crystal structure of the Chili RNA aptamer in complex with DMHBO+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine.

Mieczkowski, M.Steinmetzger, C.Bessi, I.Lenz, A.K.Schmiedel, A.Holzapfel, M.Lambert, C.Pena, V.Hobartner, C.

(2021) Nat Commun 12: 3549-3549

  • DOI: https://doi.org/10.1038/s41467-021-23932-0
  • Primary Citation of Related Structures:  
    7OA3, 7OAV, 7OAW, 7OAX

  • PubMed Abstract: 

    Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO + and DMHBI + ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.


  • Organizational Affiliation

    Julius-Maximilians-Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074, Würzburg, Germany.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Chili RNA Aptamer
A, B, C, D
52synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
BA [auth D],
E [auth A],
M [auth B],
U [auth C]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
V5Z (Subject of Investigation/LOI)
Query on V5Z

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DA [auth D],
F [auth A],
O [auth B],
W [auth C]
DMHBO+
C22 H25 N4 O5
GYWNIEJGWAVLAZ-UHFFFAOYSA-O
SPM
Query on SPM

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CA [auth D],
G [auth A],
N [auth B],
V [auth C]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
GOL
Query on GOL

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H [auth A],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K
Query on K

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AA [auth C]
FA [auth D]
GA [auth D]
HA [auth D]
J [auth A]
AA [auth C],
FA [auth D],
GA [auth D],
HA [auth D],
J [auth A],
K [auth A],
L [auth A],
Q [auth B],
R [auth B],
S [auth B],
Y [auth C],
Z [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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EA [auth D],
I [auth A],
P [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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T [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.324α = 90
b = 100.352β = 90
c = 113.294γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany682586

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description