6TR2 | pdb_00006tr2

Pre-folded structures govern folding pathways of human telomeric G-quadruplexes

• PDB DOI: https://doi.org/10.2210/pdb6TR2/pdb
• BMRB: 34467
• NAKB: 6TR2

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


• Deposited: 2019-12-17 Released: 2020-01-01 
• Deposition Author(s): Wang, B., Frelih, T., Plavec, J., Sket, P.
• 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

Pre-folded structures govern folding pathways of human telomeric G-quadruplexes.

Frelih, T., Wang, B., Plavec, J., Sket, P.

(2020) Nucleic Acids Res 48: 2189-2197

• PubMed: 31950178 
• DOI: https://doi.org/10.1093/nar/gkz1235
• Primary Citation Related Structures: 
  6TR2


• PubMed Abstract: 
  

  Understanding the mechanism by which biological macromolecules fold into their functional native conformations represents a problem of fundamental interest. DNA oligonucleotides derived from human telomeric repeat d[TAGGG(TTAGGG)3] and d[TAGGG(TTAGGG)3TT] fold into G-quadruplexes through diverse steps. Varying the pH and temperature by the use of nuclear magnetic resonance and other methods enabled detection of pre-folded structures that exist in solution before completely formed G-quadruplexes upon addition of cations. Pre-folded structures are in general hard to detect, however their knowledge is crucial to set up folding pathways into final structure since they are believed to be a starting point. Unexpectedly well-defined pre-folded structures composed of base triples for both oligonucleotides were detected at certain pH and temperature. These kinds of structures were up to now only hypothesized as intermediates in the folding process. All revealed pre-folded structures irrespective of the pH and temperature exhibited one common structural feature that could govern folding process.

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Organizational Affiliation: 
• Slovenian NMR Center, National Institute of Chemistry, Ljubljana 1000, Slovenia.
EN-FIST Center of Excellence, Ljubljana 1000, Slovenia.
Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana 1000, Slovenia.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 7.29 kDa 
• Atom Count: 485 
• Modeled Residue Count: 23 
• Deposited Residue Count: 23 
• 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*GP*G)-3')	A	23	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: 2020-01-01 
Deposition Author(s): Wang, B., Frelih, T., Plavec, J., Sket, P.

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Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-0242
Slovenian Research Agency	Slovenia	J1-7108
Slovenian Research Agency	Slovenia	J3-7245

Revision History  

• Version 1.0: 2020-01-01
  Type: Initial release
  
• Version 1.1: 2020-07-15
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references