Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 13.01 kDa 
• Atom Count: 1014 
• Modelled Residue Count: 37 
• Deposited Residue Count: 37 
• Unique nucleic acid chains: 1

6E8U

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

• DOI: 10.2210/pdb6E8U/pdb
• NDB: 6E8U

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2018-07-31 Released: 2019-04-17 
• Deposition Author(s): Trachman, R.J., Ferre-D'Amare, A.R.

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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 

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

• PubMed: 30992561 
• 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 0.55). 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.

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Organizational Affiliation: 

Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (37-MER)	A [auth B]	37	synthetic construct

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HZD (Subject of Investigation/LOI)	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
K	J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	B, C [auth B], D [auth B], E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	H [auth B], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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 = 53.27	α = 90
b = 53.27	β = 90
c = 188.036	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2018-07-31 
• Released Date: 2019-04-17 
Deposition Author(s): Trachman, R.J., Ferre-D'Amare, A.R.

Revision History  

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