BMRB Entry 34265

Name: Solution structure of the r(UGGUGGU)4 RNA quadruplex
Published: 2018-10-26

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PDB ID: 6ge1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34265
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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:

Solution structure of the r(UGGUGGU)4 RNA quadruplex

Deposition date:

2018-04-25

Original release date:

2018-10-26

Authors:

Andralojc, W.; Gdaniec, Z.

Citation:

Citation: Andralojc, W.; Malgowska, M.; Sarzynska, J.; Pasternak, K.; Szpotkowski, K.; Kierzek, R.; Gdaniec, Z.. "Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus." RNA 25, 121-134 (2019).
PubMed: 30341177

Assembly members:

Assembly members:
entity_1, polymer, 7 residues, 2254.363 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 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):
entity_1: UGGUGGU

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	44
1H chemical shifts	169
31P chemical shifts	7

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
3	entity_1, 3	1
4	entity_1, 4	1

Entities:

Entity 1, entity_1, 1 7 residues - 2254.363 Da.

1

U

G

U

G

U

Samples:

sample_1: pUGGUGGU 2.0 mM; phosphate buffer 10 mM; potassium chloride 50 mM

sample_2: pUGGUGGU 2.0 mM; phosphate buffer 10 mM; potassium chloride 0.05 mM

sample_conditions_1: ionic strength: 0.06 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.06 M; pH: 6.8; pressure: 1 atm; temperature: 278 K

sample_conditions_3: ionic strength: 0.06 M; pH: 6.8; pressure: 1 bar; temperature: 333 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_3
2D 1H-31P COSY	sample_1	isotropic	sample_conditions_3

Software:

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

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

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AvanceIII 700 MHz