BMRB Entry 16714

Name: Structure of a human Xist RNA A-repeat AUCG tetraloop hairpin essential for X-inactivation
Published: 2011-08-17

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PDB ID: 2y95
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16714
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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 a human Xist RNA A-repeat AUCG tetraloop hairpin essential for X-inactivation

Deposition date:

2010-02-09

Original release date:

2011-08-17

Authors:

Duszczyk, Malgorzata; Sattler, Michael

Citation:

Citation: Duszczyk, Malgorzata; Sattler, Michael. "H, 13C, 15N and P chemical shift assignments of a human Xist RNA A-repeat tetraloop hairpin essential for X-chromosome inactivation." Biomol. NMR Assignments 6, 75-77 (2012).
PubMed: 21779925

Assembly members:

Assembly members:
AUCG tetraloop hairpin, polymer, 14 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
AUCG tetraloop hairpin: GGCGCAUCGGCGCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2
coupling_constants
- coupling_constant_list_1
RDCs
- RDC_list_1

Data type	Count
13C chemical shifts	104
15N chemical shifts	45
1H chemical shifts	120
31P chemical shifts	13
coupling constants	42
residual dipolar couplings	29

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	AUCG tetraloop hairpin	1

Entities:

Entity 1, AUCG tetraloop hairpin 14 residues - Formula weight is not available

1

G

C

G

C

A

U

C

G

2

C

G

C

Samples:

sample_1: Xist RNA A-repeat AUCG tetraloop hairpin 1.0 mM; sodium phosphate 10 mM; sodium chloride 100 mM; EDTA 0.02 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_2: Xist RNA A-repeat AUCG tetraloop hairpin 1.2 mM; sodium phosphate 10 mM; sodium chloride 100 mM; EDTA 0.02 mM; sodium azide 0.02%; D2O 100%

sample_3: Xist RNA A-repeat AUCG tetraloop hairpin, [U-98% 13C; U-98% 15N], 0.8 – 1.2 mM; sodium phosphate 10 mM; sodium chloride 100 mM; EDTA 0.02 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_4: Xist RNA A-repeat AUCG tetraloop hairpin, [U-98% 13C; U-98% 15N], 0.8 – 1.2 mM; sodium phosphate 10 mM; sodium chloride 100 mM; EDTA 0.02 mM; sodium azide 0.02%; D2O 100%

sample_5: Xist RNA A-repeat AUCG tetraloop hairpin 1.2 mM; sodium phosphate 10 mM; sodium chloride 100 mM; EDTA 0.02 mM; sodium azide 0.02%; filamentous bacteriophage Pf1 18 mg/ml; D2O 100%

sample_6: Xist RNA A-repeat AUCG tetraloop hairpin, [U-98% 13C; U-98% 15N], 0.4 mM; Xist RNA A-repeat AUCG tetraloop hairpin 0.4 mM; sodium phosphate 10 mM; sodium chloride 100 mM; EDTA 0.02%; sodium azide 0.02 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.0; pressure: 1 atm; temperature: 278 K

sample_conditions_2: pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY with watergate and waterflipback	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
HNN-COSY	sample_3	isotropic	sample_conditions_1
HNN-COSY	sample_6	isotropic	sample_conditions_1
HNN-COSY long-range	sample_4	isotropic	sample_conditions_2
HNN-COSY with adiabatic refocusing	sample_4	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_2
2D 1H-13C HMQC	sample_4	isotropic	sample_conditions_2
3D 1H-13C NOESY-HMQC	sample_4	isotropic	sample_conditions_2
3D HCCH-COSY	sample_4	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_2
3D HCN	sample_4	isotropic	sample_conditions_2
3D HCP	sample_4	isotropic	sample_conditions_2
2D 1H-13C HC-TROSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HC-TROSY	sample_5	anisotropic	sample_conditions_2
3D HCCH-E.COSY	sample_4	isotropic	sample_conditions_2
3D forward directed HCCH-E.COSY	sample_4	isotropic	sample_conditions_2
3D HCP spin-echo-diff	sample_4	isotropic	sample_conditions_2
2D 1H-13C selective HSQC	sample_4	isotropic	sample_conditions_2
TROSY relayed HCCH-COSY	sample_4	isotropic	sample_conditions_2

Software:

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

ARIA v1.2, Linge, O'Donoghue and Nilges - structure solution

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NUChemiCS, Wijmenga, Kruithof, Hilbers - chemical shift calculation

NMR spectrometers:

Bruker DRX 900 MHz
Bruker DRX 800 MHz
Bruker DRX 600 MHz