5M2L

Structure of DNA tetrameric 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

  • Deposited: 2016-10-13 Released: 2017-05-31 
  • Deposition Author(s): Kocman, V., Plavec, J.
  • Funding Organization(s): Slovenian Research Agency 

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/ncomms15355
  • Primary Citation of Related Structures:  5M1L, 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, respec ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')A,B,C,D15Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-10-13 
  • Released Date: 2017-05-31 
  • Deposition Author(s): Kocman, V., Plavec, J.

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

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Data collection