5OGA | pdb_00005oga

Structure of minimal i-motif domain

• PDB DOI: https://doi.org/10.2210/pdb5OGA/pdb
• NAKB: 5OGA
• BMRB: 34162

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2017-07-12 Released: 2017-11-29 
• Deposition Author(s): Mir, B., Serrano, I., Buitrago, D., Orozco, M., Escaja, N., Gonzalez, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted 

Literature

Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH.

Mir, B., Serrano, I., Buitrago, D., Orozco, M., Escaja, N., Gonzalez, C.

(2017) J Am Chem Soc 139: 13985-13988

• PubMed: 28933543 
• DOI: https://doi.org/10.1021/jacs.7b07383
• Primary Citation Related Structures: 
  5OGA


• PubMed Abstract: 
  

  We report here the solution structure of several repetitive DNA sequences containing d(TCGTTCCGT) and related repeats. At physiological pH, these sequences fold into i-motif like quadruplexes in which every two repeats a globular structure is stabilized by two hemiprotonated C:C ⁺ base pairs, flanked by two minor groove tetrads resulting from the association of G:C or G:T base pairs. The interaction between the minor groove tetrads and the nearby C:C ⁺ base pairs affords a strong stabilization, which results in effective pH _T values above 7.5. Longer sequences with more than two repeats are able to fold in tandem, forming a rosary bead-like structure. Bioinformatics analysis shows that these sequences are prevalent in the human genome, and are present in development-related genes.

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Organizational Affiliation: 
• Inorganic and Organic Chemistry Department, Organic Chemistry Section, and IBUB, University of Barcelona , Martí i Franquès 1-11, 08028 Barcelona, Spain.
BIOESTRAN associated unit UB-CSIC , 08028 Barcelona, Spain.
Instituto de Química Física 'Rocasolano', CSIC , Serrano 119, 28006 Madrid, Spain.
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) , 08028 Barcelona, Spain.
Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona , Spain.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 6.28 kDa 
• Atom Count: 419 
• Modeled Residue Count: 21 
• Deposited Residue Count: 21 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*(DCP)P*GP*TP*TP*CP*(DCP)P*GP*TP*TP*TP*TP*TP*CP*GP*TP*TP*CP*CP*GP*T)-3')	A	21	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Mir, B., Serrano, I., Buitrago, D., Orozco, M., Escaja, N., Gonzalez, C.

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection
• Version 1.2: 2024-06-19
  Changes: Data collection, Database references