3LOA

Crystal Structure Analysis of the RNA construct with two adjacent ligand binding sites of helix h44 in 16S ribosomal RNA

  • Classification: RNA

  • Deposited: 2010-02-03 Released: 2010-08-04 
  • Deposition Author(s): Dibrov, S.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.299 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A model for the study of ligand binding to the ribosomal RNA helix h44.

Dibrov, S.M.Parsons, J.Hermann, T.

(2010) Nucleic Acids Res. 38: 4458-4465

  • DOI: 10.1093/nar/gkq159

  • PubMed Abstract: 
  • Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and ...

    Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicable to model RNAs, which are readily crystallized and often give rise to higher resolution crystal structures suitable for detailed analysis of ligand-RNA interactions. Here, we have investigated the HX RNA construct which contains two adjacent ligand binding regions of helix h44 in 16S ribosomal RNA. High-resolution crystal structure analysis confirmed that the HX RNA is a faithful structural model of the ribosomal target. Solution studies showed that HX RNA carrying a fluorescent 2-aminopurine modification provides a model system that can be used to monitor ligand binding to both the ribosomal decoding site and, through an indirect effect, the hygromycin B interaction region.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*CP*CP*GP*CP*GP*CP*CP*CP*GP*(5BU)P*CP*AP*CP*AP*CP*CP*AP*CP*CP*CP*G)-3'A21N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*GP*GP*GP*(5BU)P*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*UP*AP*AP*CP*GP*CP*GP*GP*C)-3'B23N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5BU
Query on 5BU
A, B
RNA LINKINGC9 H12 Br N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.299 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 57.455α = 90.00
b = 57.455β = 90.00
c = 58.433γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data collection
CNSrefinement
CNSphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-02-03 
  • Released Date: 2010-08-04 
  • Deposition Author(s): Dibrov, S.

Revision History 

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance