6GZ6

Structure of a left-handed G-quadruplex

• PDB DOI: https://doi.org/10.2210/pdb6GZ6/pdb
• NAKB: 6GZ6

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2018-07-03 Released: 2019-04-24 
• Deposition Author(s): Bakalar, B., Heddi, B., Schmitt, E., Mechulam, Y., Phan, A.T.
• Funding Organization(s): Ministry of Education (Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

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

• PubMed: 30481397 
• DOI: https://doi.org/10.1002/anie.201812628
• Primary Citation of Related Structures:  
  6FQ2, 6GZ6


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 8.69 kDa 
• Atom Count: 582 
• Modelled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	A	27	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	B [auth A], C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.57	α = 90
b = 37.63	β = 90
c = 54.28	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Bakalar, B., Heddi, B., Schmitt, E., Mechulam, Y., Phan, A.T.

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Funding Organization	Location	Grant Number
Ministry of Education (Singapore)	Singapore	MOE2015-T2-1-092
Ministry of Education (Singapore)	Singapore	MOE2012-T3-1-001

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description