6E8U

Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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This is version 1.1 of the entry. See complete history


Literature

Structure and functional reselection of the Mango-III fluorogenic RNA aptamer.

Trachman 3rd., R.J.Autour, A.Jeng, S.C.Y.Abdolahzadeh, A.Andreoni, A.Cojocaru, R.Garipov, R.Dolgosheina, E.V.Knutson, J.R.Ryckelynck, M.Unrau, P.J.Ferre-D'Amare, A.R.

(2019) Nat Chem Biol 15: 472-479

  • DOI: 10.1038/s41589-019-0267-9
  • Primary Citation of Related Structures:  
    6E8S, 6E8T, 6E8U

  • PubMed Abstract: 
  • Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0 ...

    Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Uniquely among related aptamers, Mango-III exhibits biphasic thermal melting, characteristic of molecules with tertiary structure. We report crystal structures of TO1-Biotin complexes of Mango-III, a structure-guided mutant Mango-III(A10U), and a functionally reselected mutant iMango-III. The structures reveal a globular architecture arising from an unprecedented pseudoknot-like connectivity between a G-quadruplex and an embedded non-canonical duplex. The fluorophore is restrained into a planar conformation by the G-quadruplex, a lone, long-range trans Watson-Crick pair (whose A10U mutation increases quantum yield to 0.66), and a pyrimidine perpendicular to the nucleobase planes of those motifs. The improved iMango-III and Mango-III(A10U) fluoresce ~50% brighter than enhanced green fluorescent protein, making them suitable tags for live cell RNA visualization.


    Organizational Affiliation

    Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA. adrian.ferre@nih.gov.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (37-MER)A [auth B]37synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HZD (Subject of Investigation/LOI)
Query on HZD

Download Ideal Coordinates CCD File 
G [auth B]4-[(3-{2,16-dioxo-20-[(3aR,4R,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium
C38 H50 N6 O6 S2
SGYJIWSWMOUKKZ-GTCKRINLSA-P
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
J [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B, C [auth B], D [auth B], E [auth B], F [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth B], I [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.27α = 90
b = 53.27β = 90
c = 188.036γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references