6FTU

Structure of a Quadruplex forming sequence from D. discoideum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome.

Guedin, A.Lin, L.Y.Armane, S.Lacroix, L.Mergny, J.L.Thore, S.Yatsunyk, L.A.

(2018) Nucleic Acids Res. 46: 5297-5307

  • DOI: 10.1093/nar/gky290

  • PubMed Abstract: 
  • Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249-1055). Therefore, D. d ...

    Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249-1055). Therefore, D. discoideum is a perfect model organism to investigate the relationship between the presence of G4s and their biological functions. As a first step in this investigation, we crystallized the dGGGGGAGGGGTACAGGGGTACAGGGG sequence from the putative promoter region of two divergent genes in D. discoideum. According to the crystal structure, this sequence folds into a four-quartet intramolecular antiparallel G4 with two lateral and one diagonal loops. The G-quadruplex core is further stabilized by a G-C Watson-Crick base pair and a A-T-A triad and displays high thermal stability (Tm > 90°C at 100 mM KCl). Biophysical characterization of the native sequence and loop mutants suggests that the DNA adopts the same structure in solution and in crystalline form, and that loop interactions are important for the G4 stability but not for its folding. Four-tetrad G4 structures are sparse. Thus, our work advances understanding of the structural diversity of G-quadruplexes and yields coordinates for in silico drug screening programs and G4 predictive tools.


    Organizational Affiliation

    Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA.,Inserm U1024, CNRS UMR 8197, IBENS, Paris, France.,Institute of Biophysics of the CAS, v.v.i., Kraálovopolskaá 135, 612 65 Brno, Czech Republic.,ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (26-MER)A,B,C,D,E,F,Z26Dictyostelium discoideum
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D, E, F, Z
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.060α = 90.00
b = 135.750β = 93.58
c = 55.200γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States1R15CA208676-01A1

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Data collection, Source and taxonomy
  • Version 1.2: 2018-05-09
    Type: Data collection, Database references
  • Version 1.3: 2018-05-23
    Type: Data collection
  • Version 1.4: 2018-06-13
    Type: Data collection, Database references