BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 16714

Title: Structure of a human Xist RNA A-repeat AUCG tetraloop hairpin essential for X-inactivation   PubMed: 21779925

Authors: Duszczyk, Malgorzata; Sattler, Michael

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).

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

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

Experimental source:   Production method: enzymatic semisynthesis

Entity Sequences (FASTA):
AUCG tetraloop hairpin: GGCGCAUCGGCGCC

Data sets:
Data typeCount
13C chemical shifts104
15N chemical shifts45
1H chemical shifts120
31P chemical shifts13
coupling constants42
residual dipolar couplings29

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1AUCG tetraloop hairpin1

Entities:

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

1   GGCGCAUCGG
2   CGCC

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESY with watergate and waterflipbacksample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
HNN-COSYsample_3isotropicsample_conditions_1
HNN-COSYsample_6isotropicsample_conditions_1
HNN-COSY long-rangesample_4isotropicsample_conditions_2
HNN-COSY with adiabatic refocusingsample_4isotropicsample_conditions_2
2D 1H-13C HSQCsample_2isotropicsample_conditions_2
2D 1H-13C HMQCsample_4isotropicsample_conditions_2
3D 1H-13C NOESY-HMQCsample_4isotropicsample_conditions_2
3D HCCH-COSYsample_4isotropicsample_conditions_2
3D HCCH-TOCSYsample_4isotropicsample_conditions_2
3D HCNsample_4isotropicsample_conditions_2
3D HCPsample_4isotropicsample_conditions_2
2D 1H-13C HC-TROSYsample_2isotropicsample_conditions_2
2D 1H-13C HC-TROSYsample_5anisotropicsample_conditions_2
3D HCCH-E.COSYsample_4isotropicsample_conditions_2
3D forward directed HCCH-E.COSYsample_4isotropicsample_conditions_2
3D HCP spin-echo-diffsample_4isotropicsample_conditions_2
2D 1H-13C selective HSQCsample_4isotropicsample_conditions_2
TROSY relayed HCCH-COSYsample_4isotropicsample_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, . - 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

Related Database Links:

GB M97168.1