6DB9

Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.

Shelke, S.A.Shao, Y.Laski, A.Koirala, D.Weissman, B.P.Fuller, J.R.Tan, X.Constantin, T.P.Waggoner, A.S.Bruchez, M.P.Armitage, B.A.Piccirilli, J.A.

(2018) Nat Commun 9: 4542-4542

  • DOI: 10.1038/s41467-018-06942-3
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3- ...

    The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO 3 bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO 3 fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO 3, and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure.


    Organizational Affiliation

    Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA. jpicciri@uchicago.edu.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab-Heavy-ChainH232synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab-Light-ChainL214synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA (60-MER)R60synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.78α = 90
b = 83.805β = 90
c = 109.926γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01AI081987

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence