Crystal structure of Squash RNA aptamer in complex with DFHBI-1T with iridium (III) ions

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

  • Deposited: 2020-11-28 Released: 2022-01-19 
  • Deposition Author(s): Truong, L., Ferre-D'Amare, A.R.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

  • Resolution: 2.73 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 

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The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold.

Truong, L.Kooshapur, H.Dey, S.K.Li, X.Tjandra, N.Jaffrey, S.R.Ferre-D'Amare, A.R.

(2022) Nat Chem Biol 18: 191-198

  • DOI: https://doi.org/10.1038/s41589-021-00931-2
  • Primary Citation of Related Structures:  
    7KVT, 7KVU, 7KVV

  • PubMed Abstract: 

    Squash is an RNA aptamer that strongly activates the fluorescence of small-molecule analogs of the fluorophore of green fluorescent protein (GFP). Unlike other fluorogenic aptamers, isolated de novo from random-sequence RNA, Squash was evolved from the bacterial adenine riboswitch to leverage its optimized in vivo folding and stability. We now report the 2.7-Å resolution cocrystal structure of fluorophore-bound Squash, revealing that while the overall fold of the riboswitch is preserved, the architecture of the ligand-binding core is dramatically transformed. Unlike previously characterized aptamers that activate GFP-derived fluorophores, Squash does not harbor a G-quadruplex, sandwiching its fluorophore between a base triple and a noncanonical base quadruple in a largely apolar pocket. The expanded structural core of Squash allows it to recognize unnatural fluorophores that are larger than the simple purine ligand of the parental adenine riboswitch, and suggests that stable RNA scaffolds can tolerate larger variation than has hitherto been appreciated.

  • Organizational Affiliation

    Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA.

Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Squash RNA aptamer bound to DFHBI-1T with iridium (III) ionsA [auth B]83synthetic construct
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.73 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.9α = 90
b = 103.9β = 90
c = 51.699γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection