2KZD | pdb_00002kzd

Structure of a (3+1) G-quadruplex formed by hTERT promoter sequence

• PDB DOI: https://doi.org/10.2210/pdb2KZD/pdb
• NAKB: 2KZD

• Classification: DNA
• Mutation(s): No 


• Deposited: 2010-06-16 Released: 2010-10-06 
• Deposition Author(s): Lim, K.W., Lacroix, L., Yue, D.J.E., Lim, J.K.C., Lim, J.M.W., Phan, A.T.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Coexistence of two distinct G-quadruplex conformations in the hTERT promoter

Lim, K.W., Lacroix, L., Yue, D.J.E., Lim, J.K.C., Lim, J.M.W., Phan, A.T.

(2010) J Am Chem Soc 132: 12331-12342

• PubMed: 20704263 
• DOI: https://doi.org/10.1021/ja101252n
• Primary Citation Related Structures: 
  2KZD, 2KZE


• PubMed Abstract: 
  

  The catalytic subunit of human telomerase, hTERT, actively elongates the 3' end of the telomere in most cancer cells. The hTERT promoter, which contains many guanine-rich stretches on the same DNA strand, exhibits an exceptional potential for G-quadruplex formation. Here we show that one particular G-rich sequence in this region coexists in two G-quadruplex conformations in potassium solution: a (3 + 1) and a parallel-stranded G-quadruplexes. We present the NMR solution structures of both conformations, each comprising several robust structural elements, among which include the (3 + 1) and all-parallel G-tetrad cores, single-residue double-chain-reversal loops, and a capping A.T base pair. A combination of NMR and CD techniques, complemented with sequence modifications and variations of experimental condition, allowed us to better understand the coexistence of the two G-quadruplex conformations in equilibrium and how different structural elements conspire to favor a particular form.

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Organizational Affiliation: 
• School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.37 kDa 
• Atom Count: 425 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*GP*IP*AP*GP*GP*GP*GP*CP*TP*GP*GP*GP*AP*GP*GP*GP*C)-3')	A	20	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-06 
Deposition Author(s): Lim, K.W., Lacroix, L., Yue, D.J.E., Lim, J.K.C., Lim, J.M.W., Phan, A.T.

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references