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 19387

Title: Solution structure of an intramolecular (3+1) human telomeric G-quadruplex bound to a telomestatin derivative   PubMed: 23909929

Deposition date: 2013-07-24 Original release date: 2013-08-26

Authors: Chung, Wan Jun; Heddi, Brahim; Tera, Masayuki; Iida, Keisuke; Nagasawa, Kazuo; Phan, Anh Tuan

Citation: Chung, Wan Jun; Heddi, Brahim; Tera, Masayuki; Iida, Keisuke; Nagasawa, Kazuo; Phan, Anh Tuan. "Solution structure of an intramolecular (3 + 1) human telomeric g-quadruplex bound to a telomestatin derivative."  J. Am. Chem. Soc. 135, 13495-13501 (2013).

Assembly members:
DNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), polymer, 24 residues, 7591.945 Da.
entity_L2H, non-polymer, 686.675 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*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'): TTGGGTTAGGGTTAGGGTTA GGGA

Data sets:
Data typeCount
1H chemical shifts240
31P chemical shifts23

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*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')1
2L2H2

Entities:

Entity 1, DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3') 24 residues - 7591.945 Da.

1   DTDTDGDGDGDTDTDADGDG
2   DGDTDTDADGDGDGDTDTDA
3   DGDGDGDA

Entity 2, L2H - C32 H34 N10 O8 - 686.675 Da.

1   L2H

Samples:

sample_1: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')0.2 – 2 mM; L2H0.2 – 2 mM; KPi 20 mM; KCl 70 mM

sample_2: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')0.2 – 2 mM; L2H0.2 – 2 mM; KPi 20 mM; KCl 70 mM

sample_3: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), [U-99% 13C; U-99% 15N], 0.2 mM; L2H 0.2 mM; KPi 20 mM; KCl 70 mM

sample_4: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), [U-99% 13C; U-99% 15N], 0.2 mM; L2H 0.2 mM; KPi 20 mM; KCl 70 mM

sample_5: DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), [U-4% 13C], 0.2 – 1 mM; L2H0.2 – 1 mM; KPi 20 mM; KCl 70 mM

sample_conditions_1: ionic strength: 90 mM; pH: 7; pressure: 1 atm; temperature: 310 K

sample_conditions_2: ionic strength: 90 mM; pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 40 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_2isotropicsample_conditions_3
2D 1H-1H TOCSYsample_1isotropicsample_conditions_3
2D 1H-1H NOESYsample_1isotropicsample_conditions_3
2D 1H-1H NOESYsample_2isotropicsample_conditions_3
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_3
2D 1H-13C HSQC aromaticsample_5isotropicsample_conditions_2
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_3
2D 1H-13C HSQC aliphaticsample_5isotropicsample_conditions_2
2D 1H-13C HSQC aliphaticsample_4isotropicsample_conditions_2
2D 1H-13C HSQC aromaticsample_4isotropicsample_conditions_2
1D JRHMBCsample_3isotropicsample_conditions_2
2D 1H-31P HSQCsample_2isotropicsample_conditions_3

Software:

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

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

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker AMX 600 MHz
  • Bruker AMX 700 MHz
  • Bruker AMX 400 MHz