6GZ6

Structure of a left-handed G-quadruplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.006 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A Minimal Sequence for Left-Handed G-Quadruplex Formation.

Bakalar, B.Heddi, B.Schmitt, E.Mechulam, Y.Phan, A.T.

(2019) Angew.Chem.Int.Ed.Engl. 58: 2331-2335

  • DOI: 10.1002/anie.201812628
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recently, we observed the first example of a left-handed G-quadruplex structure formed by natural DNA, named Z-G4. We analysed the Z-G4 structure and inspected its primary 28-nt sequence in order to identify motifs that convey the unique left-handed ...

    Recently, we observed the first example of a left-handed G-quadruplex structure formed by natural DNA, named Z-G4. We analysed the Z-G4 structure and inspected its primary 28-nt sequence in order to identify motifs that convey the unique left-handed twist. Using circular dichroism spectroscopy, NMR spectroscopy, and X-ray crystallography, we revealed a minimal sequence motif of 12 nt (GTGGTGGTGGTG) for formation of the left-handed DNA G-quadruplex, which is found to be highly abundant in the human genome. A systematic analysis of thymine loop mutations revealed a moderate sequence tolerance, which would further broaden the space of sequences prone to left-handed G-quadruplex formation.


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.,Laboratoire de Biologie et Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure Paris-Saclay, 94235, Cachan, France.,Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, 91128, Palaiseau, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (27-MER)A27Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.006 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 29.570α = 90.00
b = 37.630β = 90.00
c = 54.280γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (Singapore)SingaporeMOE2015-T2-1-092
Ministry of Education (Singapore)SingaporeMOE2012-T3-1-001

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release