6E80

Crystal structure of the Corn aptamer in unliganded state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.901 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence.

Sjekloca, L.Ferre-D'Amare, A.R.

(2019) Cell Chem Biol 26: 1159

  • DOI: 10.1016/j.chembiol.2019.04.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thioflavin T (ThT) is widely used for the detection of amyloids. Many unrelated DNAs and RNAs that contain G-quadruplex motifs also bind ThT and strongly activate its fluorescence. To elucidate the structural basis of ThT binding to G quadruplexes an ...

    Thioflavin T (ThT) is widely used for the detection of amyloids. Many unrelated DNAs and RNAs that contain G-quadruplex motifs also bind ThT and strongly activate its fluorescence. To elucidate the structural basis of ThT binding to G quadruplexes and its fluorescence turn-on, we determined its co-crystal structure with the homodimeric RNA Corn, which contains two G quadruplexes. We found that two ThT molecules bind in the dimer interface, constrained by a G quartet from each protomer into a maximally fluorescent planar conformation. The unliganded Corn homodimer crystal structure reveals a collapsed fluorophore-binding site. In solution, Corn must fluctuate between this and an open, binding-competent conformation. A co-crystal structure with another benzothiazole derivate, thiazole orange (TO), also shows binding at the Corn homodimer interface. As the bound ThT and TO make no interactions with the RNA backbone, their Corn co-crystal structures likely explain their fluorescence activation upon sequence-independent DNA and RNA G-quadruplex binding.


    Organizational Affiliation

    Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA. Electronic address: adrian.ferre@nih.gov.,Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (36-MER)A36synthetic construct
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
IR
Query on IR

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Download CCD File 
A
IRIDIUM ION
Ir
MOHYGSBMXIJZBJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IRI
Query on IRI

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Download CCD File 
A
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.901 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.252 
  • Space Group: H 3 2
  • Diffraction Data DOI: 
    10.15785/SBGRID/701 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 93.012α = 90.00
b = 93.012β = 90.00
c = 66.560γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-28
    Type: Data collection, Database references