4U5M

Structure of a left-handed DNA G-quadruplex

• PDB DOI: https://doi.org/10.2210/pdb4U5M/pdb
• NAKB: 4U5M

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


• Deposited: 2014-07-25 Released: 2015-02-25 
• Deposition Author(s): Schmitt, E., Mechulam, Y., Phan, A.T., Brahim, H., Chung, W.J., Lim, K.W.
• Funding Organization(s): Ministry of education, Nanyang technological university, Centre National de la Recherche Scientifique, Ecole polytechnique

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.180 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

Literature

Structure of a left-handed DNA G-quadruplex.

Chung, W.J., Heddi, B., Schmitt, E., Lim, K.W., Mechulam, Y., Phan, A.T.

(2015) Proc Natl Acad Sci U S A 112: 2729-2733

• PubMed: 25695967 
• DOI: https://doi.org/10.1073/pnas.1418718112
• Primary Citation of Related Structures:  
  4U5M


• PubMed Abstract: 
  

  Aside from the well-known double helix, DNA can also adopt an alternative four-stranded structure known as G-quadruplex. Implications of such a structure in cellular processes, as well as its therapeutic and diagnostic applications, have been reported. The G-quadruplex structure is highly polymorphic, but so far, only right-handed helical forms have been observed. Here we present the NMR solution and X-ray crystal structures of a left-handed DNA G-quadruplex. The structure displays unprecedented features that can be exploited as unique recognition elements.

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Organizational Affiliation: 

School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore; and.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 9.05 kDa 
• Atom Count: 730 
• Modelled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	B [auth A], C [auth A], D [auth A], E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.180 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.886	α = 90
b = 51.886	β = 90
c = 40.167	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Schmitt, E., Mechulam, Y., Phan, A.T., Brahim, H., Chung, W.J., Lim, K.W.

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Funding Organization	Location	Grant Number
Ministry of education	Singapore	--
Nanyang technological university	Singapore	--
Centre National de la Recherche Scientifique	France	UMR7654
Ecole polytechnique	France	UMR7654

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references
• Version 1.2: 2015-03-11
  Changes: Database references
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations