5LQG | pdb_00005lqg

A two-quartet G-quadruplex formed by human telomere in KCl solution at neutral pH

• PDB DOI: https://doi.org/10.2210/pdb5LQG/pdb
• BMRB: 34034
• NAKB: 5LQG

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


• Deposited: 2016-08-17 Released: 2018-06-13 
• Deposition Author(s): Galer, P., Wang, B., Sket, P., Plavec, J.
• Funding Organization(s): Slovenian Research Agency

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Literature

Reversible pH Switch of Two-Quartet G-Quadruplexes Formed by Human Telomere.

Galer, P., Wang, B., Sket, P., Plavec, J.

(2016) Angew Chem Int Ed Engl 55: 1993-1997

• PubMed: 26836334 
• DOI: https://doi.org/10.1002/anie.201507569
• Primary Citation Related Structures: 
  5LQG, 5LQH


• PubMed Abstract: 
  

  A four-repeat human telomere DNA sequence without the 3'-end guanine, d[TAGGG(TTAGGG)2 TTAGG] (htel1-ΔG23) has been found to adopt two distinct two G-quartet antiparallel basket-type G-quadruplexes, TD and KDH(+) in presence of KCl. NMR, CD, and UV spectroscopy have demonstrated that topology of KDH(+) form is distinctive with unique protonated T18⋅A20(+) ⋅G5 base triple and other capping structural elements that provide novel insight into structural polymorphism and heterogeneity of G-quadruplexes in general. Specific stacking interactions amongst two G-quartets flanking base triples and base pairs in TD and KDH(+) forms are reflected in 10 K higher thermal stability of KDH(+) . Populations of TD and KDH(+) forms are controlled by pH. The (de)protonation of A20 is the key for pH driven structural transformation of htel1-ΔG23. Reversibility offers possibilities for its utilization as a conformational switch within different compartments of living cell enabling specific ligand and protein interactions.

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Organizational Affiliation: 
• Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia.
Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia. [e-mail].
EN-FIST Center of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia. [e-mail].
Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia. [e-mail].
EN-FIST Center of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia. [e-mail].
Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia. [e-mail].

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 6.96 kDa 
• Atom Count: 463 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*G)-3')	A	22	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Galer, P., Wang, B., Sket, P., Plavec, J.

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Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-0242
Slovenian Research Agency	Slovenia	J1-6733
Slovenian Research Agency	Slovenia	J1-7108

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection
• Version 1.2: 2019-06-19
  Changes: Data collection
• Version 1.3: 2019-08-07
  Changes: Data collection, Database references
• Version 1.4: 2024-05-15
  Changes: Data collection, Database references