5EMF

Crystal structure of RNA r(GCUGCUGC) with antisense PNA p(GCAGCAGC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.122 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The first crystal structures of RNA-PNA duplexes and a PNA-PNA duplex containing mismatches-toward anti-sense therapy against TREDs.

Kiliszek, A.Banaszak, K.Dauter, Z.Rypniewski, W.

(2016) Nucleic Acids Res. 44: 1937-1943

  • DOI: 10.1093/nar/gkv1513
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PNA is a promising molecule for antisense therapy of trinucleotide repeat disorders. We present the first crystal structures of RNA-PNA duplexes. They contain CUG repeats, relevant to myotonic dystrophy type I, and CAG repeats associated with poly-gl ...

    PNA is a promising molecule for antisense therapy of trinucleotide repeat disorders. We present the first crystal structures of RNA-PNA duplexes. They contain CUG repeats, relevant to myotonic dystrophy type I, and CAG repeats associated with poly-glutamine diseases. We also report the first PNA-PNA duplex containing mismatches. A comparison of the PNA homoduplex and the PNA-RNA heteroduplexes reveals PNA's intrinsic structural properties, shedding light on its reported sequence selectivity or intolerance of mismatches when it interacts with nucleic acids. PNA has a much lower helical twist than RNA and the resulting duplex has an intermediate conformation. PNA retains its overall conformation while locally there is much disorder, especially peptide bond flipping. In addition to the Watson-Crick pairing, the structures contain interesting interactions between the RNA's phosphate groups and the Π electrons of the peptide bonds in PNA.


    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 (5'-R(*GP*CP*UP*GP*CP*UP*GP*C)-3')A8Homo sapiens
Entity ID: 2
MoleculeChainsLengthOrganism
antisense PNA p(GCAGCAGC)B8synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
CPN
Query on CPN
B
PEPTIDE-LIKEC10 H16 N5 O4

--

GPN
Query on GPN
B
PEPTIDE-LIKEC11 H16 N7 O4

--

APN
Query on APN
B
PEPTIDE-LIKEC11 H16 N7 O3

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.122 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 35.110α = 90.00
b = 35.110β = 90.00
c = 69.114γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACphasing
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2017-05-17
    Type: Other
  • Version 1.3: 2018-03-07
    Type: Data collection