6QIR

Crystal structure of CAG repeats with synthetic CMBL3a compound (model I)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1093/nar/gkz832
  • Primary Citation of Related Structures:  
    6QIV, 6QIQ, 6QIS, 6QIR, 6QIT

  • 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 ...

    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

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



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')A, B, C, D8Homo sapiens
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    J48
    Query on J48

    Download CCD File 
    A, C, D
    CMBL3a
    C26 H26 N7 O4
    GBOMGPRBHPRGNP-OWOJBTEDSA-O
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.53 Å
    • R-Value Free: 0.233 
    • R-Value Work: 0.177 
    • R-Value Observed: 0.179 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 77.024α = 90
    b = 46.747β = 129.72
    c = 54.811γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    XDSdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


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

    Revision History 

    • 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