BMRB Entry 34025

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34025
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
G-Quadruplex formed at the 5'-end of NHEIII_1 Element in human c-MYC promoter bound to triangulenium based fluorescence probe DAOTA-M2
Deposition date:
2016-07-14
Original release date:
2016-09-09
Authors:
Kotar, A.; Wang, B.; Shivalingam, A.; Gonzalez-Garcia, J.; Vilar, R.; Plavec, J.
Citation:

Citation: Kotar, A.; Wang, B.; Shivalingam, A.; Gonzalez-Garcia, J.; Vilar, R.; Plavec, J.. "NMR Structure of a Triangulenium-Based Long-Lived Fluorescence Probe Bound to a G-Quadruplex."  Angew. Chem. Int. Ed. Engl. 55, 12508-12511 (2016).
PubMed: 27577037

Assembly members:

Assembly members:
entity_1, polymer, 19 residues, 6070.918 Da.
entity_6XM, non-polymer, 510.627 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TAGGGAGGGTAGGGAGGGT

Data sets:
Data typeCount
1H chemical shifts138

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_2, 12
3entity_2, 22

Entities:

Entity 1, entity_1 19 residues - 6070.918 Da.

1   DTDADGDGDGDADGDGDGDT
2   DADGDGDGDADGDGDGDT

Entity 2, entity_2, 1 - C31 H34 N4 O3 - 510.627 Da.

1   6XM

Samples:

sample_1: DAOTA-M2 0.4 mM; DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3') 0.2 mM; potassium chloride 100 mM; potassium phosphate 20 mM

sample_2: DAOTA-M2 0.4 mM; DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3') 0.2 mM; LITHIUM CACODYLATE 10 mM; potassium chloride 100 mM

sample_3: DAOTA-M2 0.4 mM; DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3') 0.2 mM; potassium chloride 100 mM; potassium phosphate 20 mM

sample_4: DAOTA-M2 0.4 mM; DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), U-8% 15N, U-8 %13C, 0.2 mM; potassium chloride 100 mM; potassium phosphate 20 mM

sample_conditions_1: ionic strength: 145 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 140 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_3anisotropicsample_conditions_2
2D 1H-1H TOCSYsample_3anisotropicsample_conditions_1
2D 1H-1H NOESYsample_1anisotropicsample_conditions_2
2D 1H-1H NOESYsample_2anisotropicsample_conditions_1
2D 1H-1H DQF_COSYsample_3anisotropicsample_conditions_2
2D 1H-31P COSYsample_3anisotropicsample_conditions_2
13C HSQCsample_4anisotropicsample_conditions_2
15N HSQCsample_4anisotropicsample_conditions_2
2D 1H-13C HSQCsample_2anisotropicsample_conditions_2

Software:

AMBER v14, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

VNMR, Varian - collection, processing

NMR spectrometers:

  • AGILENT-VARIAN UNIFORM NMR SYSTEM 600 MHz
  • AGILENT-VARIAN UNIFORM NMR SYSTEM 800 MHz