6QIV

Crystal structure of seleno-derivative CAG repeats with synthetic CMBL4 compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 

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:  

  • 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 Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria.,Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka, Ibaraki 567-0047, Japan.,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*AP*GP*CP*AP*GP*C)-3')A8Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J4H
Query on J4H

Download SDF File 
Download CCD File 
A
CMBL4
C26 H29 N8 O4
XPQLVLKMYDQLQU-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 37.503α = 90.00
b = 37.503β = 90.00
c = 38.334γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PHENIXrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Center for Research and Development (Poland)PolandNCN 2017/26/E/NZ1/00950

Revision History 

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