BMRB Entry 34051

Name: Structure of DNA AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene
Published: 2017-05-25

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PDB ID: 5m1l
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34051
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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:

Structure of DNA AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene

Deposition date:

2016-10-09

Original release date:

2017-05-25

Authors:

Kocman, V.; Plavec, J.

Citation:

Citation: Kocman, V.; Plavec, J.. "Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions." Nat. Commun. 8, 15355-15355 (2017).
PubMed: 28513602

Assembly members:

Assembly members:
entity_1, polymer, 15 residues, 4765.084 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: GCGAGGGAGCGAGGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	137

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, 1	1
2	entity_1, 2	1

Entities:

Entity 1, entity_1, 1 15 residues - 4765.084 Da.

1

DG

DC

DG

DA

DG

DA

DG

DC

2

DG

DA

DG

Samples:

sample_1: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3') 0.8 mM

sample_2: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), [10 % 15N] residue specific Gua, 0.8 mM

sample_3: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), [10% 13C] residues specific adenine, 0.8 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.25; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
1D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1

Software:

AMBER 14, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman - refinement, structure calculation

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Agilent-Varian Uniform NMR System 600 MHz
Agilent-Varian Uniform NMR System 800 MHz