6DB9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.025 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.0 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
  • Primary Citation of Related Structures:  

  • 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.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.,Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA. jpicciri@uchicago.edu.,Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA. jpicciri@uchicago.edu.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab-Heavy-Chain
H
232N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab-Light-Chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
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 SDF File 
Download CCD File 
R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.025 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.780α = 90.00
b = 83.805β = 90.00
c = 109.926γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01AI081987

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release