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 25378

Title: A structure of G-quadruplex   PubMed: 26400177

Authors: Cheong, Vee Vee; Heddi, Brahim; Lech, Christopher; Phan, Anh Tuan

Citation: Cheong, Vee Vee; Heddi, Brahim; Lech, Christopher; Phan, Anh Tuan. "Xanthine and 8-oxoguanine in G-quadruplexes: formation of a GGXO tetrad"  Nucleic Acids Res. 43, 10506-10514 (2015).

Assembly members:
DNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3'), polymer, 24 residues, 7259.721 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
DNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3'): TTGGGTTAXGGTTAGGXTTA GGGA

Data sets:
Data typeCount
1H chemical shifts232

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3')1

Entities:

Entity 1, DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3') 24 residues - 7259.721 Da.

1   DTDTDGDGDGDTDTDA8OGDG
2   DGDTDTDADGDG3ZODTDTDA
3   DGDGDGDA

Samples:

sample_1: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*(8OG)P*GP*GP*TP*TP*AP*GP*GP*(3ZO)P*TP*TP*AP*GP*GP*GP*A)-3') 0.7 mM; potassium phosphate 20 mM; potassium chloride 70 mM

sample_conditions_1: ionic strength: 90 mM; pH: 8.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1

Software:

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

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

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

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 700 MHz

Related Database Links: