Crystal structure of seleno-derivative CAG repeats with synthetic CMBL3a compound

Experimental Data Snapshot

  • Resolution: 2.52 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats.

Mukherjee, S.Blaszczyk, L.Rypniewski, W.Falschlunger, C.Micura, R.Murata, A.Dohno, C.Nakatani, K.Kiliszek, A.

(2019) Nucleic Acids Res 47: 10906-10913

  • DOI: https://doi.org/10.1093/nar/gkz832
  • Primary Citation of Related Structures:  
    6QIQ, 6QIR, 6QIS, 6QIT, 6QIV

  • PubMed Abstract: 

    The trinucleotide repeat expansion disorders (TREDs) constitute of a group of >40 hereditary neurodegenerative human diseases associated with abnormal expansion of repeated sequences, such as CAG repeats. The pathogenic factor is a transcribed RNA or protein whose function in the cell is compromised. The disorders are progressive and incurable. Consequently, many ongoing studies are oriented at developing therapies. We have analyzed crystal structures of RNA containing CAG repeats in complex with synthetic cyclic mismatch-binding ligands (CMBLs). The models show well-defined interactions between the molecules in which the CMBLs mimic nucleobases as they form pseudo-canonical base pairs with adenosine residues and engage in extensive stacking interactions with neighboring nucleotides. The binding of ligands is associated with major structural changes of the CAG repeats, which is consistent with results of biochemical studies. The results constitute an early characterization of the first lead compounds in the search for therapy against TREDs. The crystallographic data indicate how the compounds could be further refined in future biomedical studies.

  • Organizational Affiliation

    Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki 567-0047, Japan.


Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*CP*AP*G)-D(P*(CSL))-R(P*AP*GP*C)-3')
A, B
8Homo sapiens
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.52 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.866α = 90
b = 46.866β = 90
c = 214.028γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
PolandNCN 2017/26/E/NZ1/00950

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references