5MWI

Crystal structure of G(CUG)8G duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Stabilization of RNA hairpins using non-nucleotide linkers and circularization.

Kiliszek, A.Blaszczyk, L.Kierzek, R.Rypniewski, W.

(2017) Nucleic Acids Res. 45: e92-e92

  • DOI: 10.1093/nar/gkx122

  • PubMed Abstract: 
  • An RNA hairpin is an essential structural element of RNA. Hairpins play crucial roles in gene expression and intermolecular recognition but are also involved in the pathogenesis of some congenital diseases. Structural studies of the hairpin motifs ar ...

    An RNA hairpin is an essential structural element of RNA. Hairpins play crucial roles in gene expression and intermolecular recognition but are also involved in the pathogenesis of some congenital diseases. Structural studies of the hairpin motifs are impeded by their thermodynamic instability, as they tend to unfold to form duplexes, especially at high concentrations required for crystallography or nuclear magnetic resonance spectroscopy. We have elaborated techniques to stabilize the RNA hairpins by linking the free ends of the RNA strand at the base of the hairpin stem. One method involves stilbene diether or hexaethylene glycol linkers and circularization by T4 RNA ligase. Another method uses click chemistry to stitch the RNA ends with a triazole linker. Both techniques are efficient and easy to perform. They should be useful in making stable, biologically relevant RNA constructs for structural studies.


    Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA G(CUG)8C duplexA26Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.192 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 43.514α = 90.00
b = 43.514β = 90.00
c = 198.101γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Science CentrePolandUMO-2011/01/B/NZ1/04429
Ministry of Science and Higher EducationPoland0450/IP1/2013/72

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references
  • Version 1.2: 2017-06-14
    Type: Database references