6QJO | pdb_00006qjo

DNA containing both right- and left-handed parallel-stranded G-quadruplexes

• PDB DOI: https://doi.org/10.2210/pdb6QJO/pdb
• NAKB: 6QJO

• Classification: DNA
• Organism(s): synthetic construct
• Expression System: synthetic construct
• Mutation(s): No 


• Deposited: 2019-01-24 Released: 2019-07-03 
• Deposition Author(s): Winnerdy, F.R., Bakalar, B., Maity, A., Vandana, J.J., Schmitt, E., Mechulam, Y., Phan, A.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.202 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

NMR solution and X-ray crystal structures of a DNA molecule containing both right- and left-handed parallel-stranded G-quadruplexes.

Winnerdy, F.R., Bakalar, B., Maity, A., Vandana, J.J., Mechulam, Y., Schmitt, E., Phan, A.T.

(2019) Nucleic Acids Res 47: 8272-8281

• PubMed: 31216034 
• DOI: https://doi.org/10.1093/nar/gkz349
• Primary Citation Related Structures: 
  6JCE, 6QJO


• PubMed Abstract: 
  

  Analogous to the B- and Z-DNA structures in double-helix DNA, there exist both right- and left-handed quadruple-helix (G-quadruplex) DNA. Numerous conformations of right-handed and a few left-handed G-quadruplexes were previously observed, yet they were always identified separately. Here, we present the NMR solution and X-ray crystal structures of a right- and left-handed hybrid G-quadruplex. The structure reveals a stacking interaction between two G-quadruplex blocks with different helical orientations and displays features of both right- and left-handed G-quadruplexes. An analysis of loop mutations suggests that single-nucleotide loops are preferred or even required for the left-handed G-quadruplex formation. The discovery of a right- and left-handed hybrid G-quadruplex further expands the polymorphism of G-quadruplexes and is potentially useful in designing a left-to-right junction in G-quadruplex engineering.

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Organizational Affiliation: 
• School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, Palaiseau 91128, France.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.18 kDa 
• Atom Count: 2,545 
• Modeled Residue Count: 112 
• Deposited Residue Count: 112 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (28-MER)	A, B, C, D	28	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C], O [auth C], P [auth D], Q [auth D], R [auth D], S [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.202 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.12	α = 90.04
b = 39.27	β = 93.03
c = 53.55	γ = 89.95

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Winnerdy, F.R., Bakalar, B., Maity, A., Vandana, J.J., Schmitt, E., Mechulam, Y., Phan, A.T.

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2019-09-18
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description