BMRB Entry 36116

Name: The structure of a chair-type G-quadruplex of the human telomeric variant in K+ solution
Published: 2018-09-24

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PDB ID: 5yey
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36116
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: The structure of a chair-type G-quadruplex of the human telomeric variant in K+ solution PubMed: 30713633

Deposition date: 2017-09-20 Original release date: 2018-09-24

Authors: Liu, C.; Zhou, B.; Kuryavyi, V.; Zhu, G.

Citation: Liu, Changdong; Zhou, Bo; Geng, Yanyan; Yan Tam, Dick; Feng, Rui; Miao, Haitao; Xu, Naining; Shi, Xiao; You, Yingying; Hong, Yuning; Tang, Ben Zhong; Kwan Lo, Pik; Kuryavyi, Vitaly; Zhu, Guang. "A chair-type G-quadruplex structure formed by a human telomeric variant DNA in K" Chem. Sci. 10, 218-226 (2019).

Assembly members:
DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3'), polymer, 21 residues, 6661.276 Da.

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

Experimental source: Production method: chemical synthesis

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

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	175

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 21 residues - 6661.276 Da.

1

DG

DT

DA

DG

DT

2

DT

DA

DG

DT

DG

3

DG

Samples:

sample_1: DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3') 2.5 mM; Potassium Phosphate 20 mM; KCl 70 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*G)-3') 2.5 mM; Potassium Phosphate 20 mM; KCl 70 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 90 mM; pH: 7; pressure: 1 atm; temperature: 284 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift calculation

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

VNMR, Varian - collection

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

NMR spectrometers:

Varian INOVA 800 MHz
Varian INOVA 500 MHz