BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 25746

Title: G-quadruplex structure   PubMed: 26673723

Authors: Heddi, Brahim; Martin-Pintado, Nerea; Serimbetov, Zhalgas; Kari, Teuku; Phan, Anh Tuan

Citation: Heddi, Brahim; Martin-Pintado, Nerea; Serimbetov, Zhalgas; Kari, Teuku; Phan, Anh Tuan. "G-quadruplexes with (4n - 1) guanines in the G-tetrad core: formation of a G-triadwater complex and implication for small-molecule binding"  Nucleic Acids Res. 44, 910-916 (2016).

Assembly members:
DNA_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3'), polymer, 18 residues, 5705.705 Da.

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
DNA_(5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3'): TTGTGTGGGTGGGTGGGT

Data sets:
Data typeCount
1H chemical shifts114

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')1

Entities:

Entity 1, DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') 18 residues - 5705.705 Da.

1   DTDTDGDTDGDTDGDGDGDT
2   DGDGDGDTDGDGDGDT

Samples:

sample_1: DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')0.1 – 1.2 mM; H2O 90%; D2O 10%

sample_2: DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3'), [U-4% 15N], 0.2-0.4 mM; H2O 90%; D2O 10%

sample_3: DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3') 0.6-1.2 mM; D2O 100%

sample_4: DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3'), [U-100% 2H], 0.2-0.4 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 45 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
2D 1H-1H HMBCsample_1isotropicsample_conditions_1
1D 15N-filtered 1H NMRsample_2isotropicsample_conditions_1
1D 1H NMRsample_4isotropicsample_conditions_1
1D 1H NMRsample_1isotropicsample_conditions_1

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution

SPARKY, Goddard - chemical shift assignment, chemical shift calculation, data analysis, peak picking

TOPSPIN, Bruker Biospin - collection

X-PLOR, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement

Spinworks, http://home.cc.umanitoba.ca/~wolowiec/spinworks - data analysis

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 700 MHz

Related Database Links: