BMRB Entry 34168

Name: G-quadruplex structure of DNA oligonucleotide containing GGGGCC repeats linked to ALS and FTD
Published: 2018-08-24

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PDB ID: 5oph
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34168
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

G-quadruplex structure of DNA oligonucleotide containing GGGGCC repeats linked to ALS and FTD

Deposition date:

2017-08-09

Original release date:

2018-08-24

Authors:

Brcic, J.; Plavec, J.

Citation:

Citation: Brcic, J.; Plavec, J.. "NMR structure of a G-quadruplex formed by four d(G4C2) repeats: insights into structural polymorphism" Nucleic Acids Res. 46, 11605-11617 (2018).
PubMed: 30277522

Assembly members:

Assembly members:
entity_1, polymer, 22 residues, 7036.323 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: GGGGCCGGGGCCGGGGCCGG XG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	176

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 22 residues - 7036.323 Da.

1

DG

DC

DG

2

DC

DG

DC

DG

3

BGM

DG

Samples:

sample_1: entity_1 1.0 mM; potassium chloride 30 mM; potassium phosphate 20 mM

sample_2: entity_1 0.4 mM; potassium chloride 30 mM; potassium phosphate 20 mM

sample_3: entity_1, one guanine in the sequence labeled 5% 15N and 13 C, 0.3 mM; potassium chloride 30 mM; potassium phosphate 20 mM

sample_conditions_1: ionic strength: 53 mM; pH: 5.8; pressure: 1 bar; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
1D 15N-edited HSQC	sample_3	isotropic	sample_conditions_1
1D 13C-edited HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1

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 - processing

NMR spectrometers:

Agilent-Varian VNMRS 600 MHz
Agilent-Varian VNMRS 800 MHz