BMRB Entry 19594

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19594
MolProbity Validation Chart

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Title:
Solution structure of a G-quadruplex bound to the bisquinolinium compound Phen-DC3
Deposition date:
2013-11-01
Original release date:
2014-01-21
Authors:
Chung, Wan Jun; Heddi, Brahim; Hamon, Florian; Teulade-Fichou, Marie-Paule; Phan, Anh Tuan
Citation:

Citation: Chung, Wan Jun; Heddi, Brahim; Hamon, Florian; Teulade-Fichou, Marie-Paule; Phan, Anh Tuan. "Solution Structure of a G-quadruplex Bound to the Bisquinolinium Compound Phen-DC3."  Angew. Chem. Int. Ed. Engl. 53, 999-1002 (2014).
PubMed: 24356977

Assembly members:

Assembly members:
DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3'), polymer, 24 residues, 7691.996 Da.
entity_PQ3, non-polymer, 550.609 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3'): TGAGGGTGGTGAGGGTGGGG AAGG

Data sets:
Data typeCount
1H chemical shifts194

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3')1
2PQ32

Entities:

Entity 1, DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3') 24 residues - 7691.996 Da.

1   DTDGDADGDGDGDTDGDGDT
2   DGDADGDGDGDTDGDGDGDG
3   DADADGDG

Entity 2, PQ3 - C34 H26 N6 O2 - 550.609 Da.

1   PQ3

Samples:

sample_1: DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3')0.2 – 2 mM; PQ30.2 – 2 mM

sample_3: DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3') 1 mM; PQ3, [U-100% 13C]-CH3, 1 mM

sample_2: DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3')0.2 – 2 mM; PQ30.2 – 2 mM

sample_conditions_1: ionic strength: 90 mM; pH: 7; temperature: 298 K

sample_conditions_2: ionic strength: 45 mM; pH: 7; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 13C-filtered HSQC-NOESYsample_3isotropicsample_conditions_1

Software:

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

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

TOPSPIN, Bruker Biospin - collection, processing

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

NMR spectrometers:

  • Bruker AMX 600 MHz
  • Bruker AMX 700 MHz