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 
  • R-Value Observed: 0.124 

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:  
    5EME, 5EMF, 5EMG

  • 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-glutamine diseases ...

    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 wojtekr@ibch.poznan.pl.



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*CP*UP*GP*CP*UP*GP*C)-3')A8Homo sapiens
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
antisense PNA p(GCAGCAGC)B8synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.124 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.11α = 90
b = 35.11β = 90
c = 69.114γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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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  (Full details and data files)

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