4U6M

Crystal structure of DNA/RNA duplex obtained in the presence of Spermine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.206 

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This is version 1.3 of the entry. See complete history. 


Literature

The crystal structure of a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer in complex with the target RNA.

Kondo, J., Nomura, Y., Kitahara, Y., Obika, S., Torigoe, H.

(2016) Chem Commun (Camb) 52: 2354-2357

  • DOI: https://doi.org/10.1039/c5cc08300a
  • Primary Citation of Related Structures:  
    4U6K, 4U6L, 4U6M

  • PubMed Abstract: 

    It has been confirmed by our previous studies that a 2',4'-BNA(NC)[N-Me]-modified antisense gapmer displays high affinity and selectivity to the target RNA strand, promising mRNA inhibitory activity and excellent nuclease resistance. Herein, we have obtained a crystal structure that provides insights into these excellent antisense properties.

    • Organizational Affiliation: 

    Department of Materials and Life Sciences, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan. j.kondo@sophia.ac.jp.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')9synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3')9synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.206 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.09α = 90
b = 49.09β = 90
c = 45.99γ = 120
Software Package:
Software NamePurpose
CrystalCleardata reduction
PHENIXphasing
CNSrefinement
PDB_EXTRACTdata extraction
PHASERmodel building
d*TREKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.2: 2022-07-06
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description