7OQT | pdb_00007oqt

G-quadruplex structure of the C. elegans telomeric repeat: A two tetrads basket type conformation stabilised by a Hoogsteen C-T base-pair

• PDB DOI: https://doi.org/10.2210/pdb7OQT/pdb
• NAKB: 7OQT
• BMRB: 34631

• Classification: DNA
• Organism(s): Caenorhabditis elegans
• Mutation(s): No 


• Deposited: 2021-06-04 Released: 2022-06-22 
• Deposition Author(s): Marquevielle, J., De Rache, A., Amrane, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 750 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

G-quadruplex structure of the C. elegans telomeric repeat: a two tetrads basket type conformation stabilized by a non-canonical C-T base-pair.

Marquevielle, J., De Rache, A., Vialet, B., Morvan, E., Mergny, J.L., Amrane, S.

(2022) Nucleic Acids Res 50: 7134-7146

• PubMed: 35736226 
• DOI: https://doi.org/10.1093/nar/gkac523
• Primary Citation Related Structures: 
  7OQT


• PubMed Abstract: 
  

  The Caenorhabditis elegans model has greatly contributed to the understanding of the role of G-quadruplexes in genomic instability. The GGCTTA repeats of the C. elegans telomeres resemble the GGGTTA repeats of the human telomeres. However, the comparison of telomeric sequences (Homo sapiens, Tetrahymena, Oxytricha, Bombyx mori and Giardia) revealed that small changes in these repeats can drastically change the topology of the folded G-quadruplex. In the present work we determined the structure adopted by the C. elegans telomeric sequence d[GG(CTTAGG)3]. The investigated C. elegans telomeric sequence is shown to fold into an intramolecular two G-tetrads basket type G-quadruplex structure that includes a C-T base pair in the diagonal loop. This work sheds light on the telomeric structure of the widely used C. elegans animal model.

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Organizational Affiliation: 
• Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA laboratory, 146 rue Léo Saignat F-33000 Bordeaux, France.
Institut Européen de Chimie et Biologie, UMS 3033 US001, CNRS-Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France.
Department of Chemistry, UNamur, 61 rue de Bruxelles, B-5000 Namur, Belgium.
Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 6.26 kDa 
• Atom Count: 414 
• 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(*GP*GP*CP*TP*TP*AP*GP*GP*CP*TP*TP*AP*GP*GP*CP*TP*TP*AP*GP*G)-3')	A	20	Caenorhabditis elegans

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K (Subject of Investigation/LOI)	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 750 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Marquevielle, J., De Rache, A., Amrane, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2022-07-06
  Changes: Database references
• Version 1.2: 2022-11-30
  Changes: Database references
• Version 1.3: 2023-06-14
  Changes: Other
• Version 1.4: 2024-06-19
  Changes: Data collection, Database references