5M1L

Structure of DNA AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene

  • Classification: DNA
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2016-10-09 Released: 2017-05-31 
  • Deposition Author(s): Kocman, V., Plavec, J.
  • Funding Organization(s): Slovenian Research Agency

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 10 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions.

Kocman, V.Plavec, J.

(2017) Nat Commun 8: 15355-15355

  • DOI: https://doi.org/10.1038/ncomms15355
  • Primary Citation of Related Structures:  
    5M1L, 5M2L, 5M4W

  • PubMed Abstract: 

    Here we describe AGCGA-quadruplexes, an unexpected addition to the well-known tetrahelical families, G-quadruplexes and i-motifs, that have been a focus of intense research due to their potential biological impact in G- and C-rich DNA regions, respectively. High-resolution structures determined by solution-state nuclear magnetic resonance (NMR) spectroscopy demonstrate that AGCGA-quadruplexes comprise four 5'-AGCGA-3' tracts and are stabilized by G-A and G-C base pairs forming GAGA- and GCGC-quartets, respectively. Residues in the core of the structure are connected with edge-type loops. Sequences of alternating 5'-AGCGA-3' and 5'-GGG-3' repeats could be expected to form G-quadruplexes, but are shown herein to form AGCGA-quadruplexes instead. Unique structural features of AGCGA-quadruplexes together with lower sensitivity to cation and pH variation imply their potential biological relevance in regulatory regions of genes responsible for basic cellular processes that are related to neurological disorders, cancer and abnormalities in bone and cartilage development.


  • Organizational Affiliation

    Slovenian NMR Centre, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')
A, B
15Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 10 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Slovenian Research AgencySloveniaP1-0242
Slovenian Research AgencySloveniaJ1-6733

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2019-05-08
    Changes: Data collection