2L88

Solution structure of all parallel G-quadruplex formed by the oncogene RET promoter sequence

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2011-01-06 Released: 2011-05-25 
  • Deposition Author(s): Tong, X., Cao, C.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Solution structure of all parallel G-quadruplex formed by the oncogene RET promoter sequence

Tong, X.Lan, W.Zhang, X.Wu, H.Liu, M.Cao, C.

(2011) Nucleic Acids Res 39: 6753-6763

  • DOI: 10.1093/nar/gkr233
  • Primary Citation of Related Structures:  
    2L88

  • PubMed Abstract: 
  • RET protein functions as a receptor-type tyrosine kinase and has been found to be aberrantly expressed in a wide range of human diseases. A highly GC-rich region upstream of the promoter plays an important role in the transcriptional regulation of RE ...

    RET protein functions as a receptor-type tyrosine kinase and has been found to be aberrantly expressed in a wide range of human diseases. A highly GC-rich region upstream of the promoter plays an important role in the transcriptional regulation of RET. Here, we report the NMR solution structure of the major intramolecular G-quadruplex formed on the G-rich strand of this region in K(+) solution. The overall G-quadruplex is composed of three stacked G-tetrad and four syn guanines, which shows distinct features for all parallel-stranded folding topology. The core structure contains one G-tetrad with all syn guanines and two other with all anti-guanines. There are three double-chain reversal loops: the first and the third loops are made of 3 nt G-C-G segments, while the second one contains only 1 nt C10. These loops interact with the core G-tetrads in a specific way that defines and stabilizes the overall G-quadruplex structure and their conformations are in accord with the experimental mutations. The distinct RET promoter G-quadruplex structure suggests that it can be specifically involved in gene regulation and can be an attractive target for pathway-specific drug design.


    Organizational Affiliation

    State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China. tongxt@mail.sioc.ac.cn



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*GP*GP*GP*GP*T)-3'A20N/A
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 100 
    • Conformers Submitted: 10 
    • Selection Criteria: structures with the lowest energy 
    • OLDERADO: 2L88 Olderado

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2011-01-06 
    • Released Date: 2011-05-25 
    • Deposition Author(s): Tong, X., Cao, C.

    Revision History 

    • Version 1.0: 2011-05-25
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2011-12-28
      Changes: Database references