5T3K

Fluorescence detection of RNA-ligand binding and crystal structure determination of ribosomal decoding site RNA using a heavy atom containing fluorescent ribonucleoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.142 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe.

Nuthanakanti, A.Boerneke, M.A.Hermann, T.Srivatsan, S.G.

(2017) Angew. Chem. Int. Ed. Engl. 56: 2640-2644

  • DOI: 10.1002/anie.201611700

  • PubMed Abstract: 
  • Comprehensive understanding of the structure-function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunc ...

    Comprehensive understanding of the structure-function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunctional nucleoside probe, containing a conformation-sensitive fluorophore and an anomalous X-ray diffraction label (5-selenophene uracil), which enables the correlation of RNA conformation and recognition under equilibrium and in 3D. The probe incorporated into the bacterial ribosomal RNA decoding site, fluorescently reports antibiotic binding and provides diffraction information in determining the structure without distorting native RNA fold. Further, by comparing solution binding data and crystal structure, we gained insight on how the probe senses ligand-induced conformational change in RNA. Taken together, our nucleoside probe represents a new class of biophysical tool that would complement available tools for functional RNA investigations.


    Organizational Affiliation

    Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*UP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*CP*UP*GP*G)-3')A,C17synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*AP*GP*CP*GP*(75B)P*CP*AP*CP*AP*CP*CP*AP*CP*CP*C)-3')B,D16synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
75B
Query on 75B
B, D
RNA linkingC13 H15 N2 O9 P SeU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.142 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 31.553α = 90.00
b = 86.956β = 94.14
c = 32.564γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release