6DB9 | pdb_00006db9

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

• PDB DOI: https://doi.org/10.2210/pdb6DB9/pdb
• NAKB: 6DB9

• Classification: RNA/Immune System
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-02 Released: 2018-11-14 
• Deposition Author(s): Shao, Y., Shelke, S.A., Laski, A., Piccirilli, J.A.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

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

• PubMed: 30382099 
• DOI: https://doi.org/10.1038/s41467-018-06942-3
• Primary Citation Related Structures: 
  6DB8, 6DB9


• 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 BL3-6 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.

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Organizational Affiliation: 
• 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.
Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
Department of Biological Sciences, 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. [e-mail].
Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.38 kDa 
• Atom Count: 4,682 
• Modeled Residue Count: 488 
• Deposited Residue Count: 506 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-Heavy-Chain	B [auth H]	232	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-Light-Chain	C [auth L]	214	synthetic construct	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (60-MER)	A [auth R]	60	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth R], E [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.78	α = 90
b = 83.805	β = 90
c = 109.926	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-14 
Deposition Author(s): Shao, Y., Shelke, S.A., Laski, A., Piccirilli, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01AI081987

Revision History  

• Version 1.0: 2018-11-14
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary