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Structure of a human Xist RNA A-repeat AUCG tetraloop hairpin essential for X-inactivation
Authors
Duszczyk, M.M., Sattler, M.
Assembly
AUCG tetraloop hairpin
Entity
1. AUCG tetraloop hairpin (polymer, Thiol state: not present), 14 monomers, 4555.711 Da Detail

GGCGCAUCGG CGCC


Formula weight
4555.711 Da
Source organism
Homo sapiens
Exptl. method
solution NMR
Data set
assigned_chemical_shifts, coupling_constants, RDCs
Chem. Shift Complete1
Sequence coverage: 64.3 %, Completeness: 7.6 %, Completeness (bb): 0.0 % Detail

Polymer type: polyribonucleotide

Total1H13C15N31P
All 7.6 % (18 of 238)11.2 % (14 of 125) 0.0 % (0 of 92)57.1 % (4 of 7) 0.0 % (0 of 14)
Suger, PO4 0.0 % (0 of 168) 0.0 % (0 of 84) 0.0 % (0 of 70) 0.0 % (0 of 14)
Nucleobase25.7 % (18 of 70)34.1 % (14 of 41) 0.0 % (0 of 22)57.1 % (4 of 7)
Aromatic13.8 % (8 of 58)13.8 % (4 of 29) 0.0 % (0 of 22)57.1 % (4 of 7)

1. AUCG tetraloop hairpin

GGCGCAUCGG CGCC

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.0


#NameIsotope labelingTypeConcentration
1Xist RNA A-repeat AUCG tetraloop hairpinnatural abundance1.0 mM
2sodium phosphatenatural abundance10 mM
3sodium chloridenatural abundance100 mM
4EDTAnatural abundance0.02 mM
5sodium azidenatural abundance0.02 %
6H2Onatural abundance90 %
7D2Onatural abundance10 %
Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.0


#NameIsotope labelingTypeConcentration
8Xist RNA A-repeat AUCG tetraloop hairpinnatural abundance1.2 mM
9sodium phosphatenatural abundance10 mM
10sodium chloridenatural abundance100 mM
11EDTAnatural abundance0.02 mM
12sodium azidenatural abundance0.02 %
13D2Onatural abundance100 %
Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.0


#NameIsotope labelingTypeConcentration
14Xist RNA A-repeat AUCG tetraloop hairpin[U-98% 13C; U-98% 15N]0.8 ~ 1.2 mM
15sodium phosphatenatural abundance10 mM
16sodium chloridenatural abundance100 mM
17EDTAnatural abundance0.02 mM
18sodium azidenatural abundance0.02 %
19H2Onatural abundance90 %
20D2Onatural abundance10 %
Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.0


#NameIsotope labelingTypeConcentration
21Xist RNA A-repeat AUCG tetraloop hairpin[U-98% 13C; U-98% 15N]0.8 ~ 1.2 mM
22sodium phosphatenatural abundance10 mM
23sodium chloridenatural abundance100 mM
24EDTAnatural abundance0.02 mM
25sodium azidenatural abundance0.02 %
26D2Onatural abundance100 %
Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.0


#NameIsotope labelingTypeConcentration
27Xist RNA A-repeat AUCG tetraloop hairpinnatural abundance1.2 mM
28sodium phosphatenatural abundance10 mM
29sodium chloridenatural abundance100 mM
30EDTAnatural abundance0.02 mM
31sodium azidenatural abundance0.02 %
32filamentous bacteriophage Pf1natural abundance18 mg/mL
33D2Onatural abundance100 %
Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.0, Details sample 50% isotope labeled, 50% unlabeled


#NameIsotope labelingTypeConcentration
34Xist RNA A-repeat AUCG tetraloop hairpin[U-98% 13C; U-98% 15N]0.4 mM
35Xist RNA A-repeat AUCG tetraloop hairpinnatural abundance0.4 mM
36sodium phosphatenatural abundance10 mM
37sodium chloridenatural abundance100 mM
38EDTAnatural abundance0.02 %
39sodium azidenatural abundance0.02 mM
40H2Onatural abundance90 %
41D2Onatural abundance10 %

Chem. Shift Complete2
Sequence coverage: 100.0 %, Completeness: 48.5 %, Completeness (bb): 48.8 % Detail

Polymer type: polyribonucleotide

Total1H13C15N31P
All48.5 % (231 of 476)47.2 % (118 of 250)49.5 % (91 of 184)64.3 % (9 of 14)46.4 % (13 of 28)
Suger, PO448.8 % (164 of 336)48.8 % (82 of 168)49.3 % (69 of 140)46.4 % (13 of 28)
Nucleobase47.9 % (67 of 140)43.9 % (36 of 82)50.0 % (22 of 44)64.3 % (9 of 14)
Aromatic49.1 % (57 of 116)44.8 % (26 of 58)50.0 % (22 of 44)64.3 % (9 of 14)

1. AUCG tetraloop hairpin

GGCGCAUCGG CGCC

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0


#NameIsotope labelingTypeConcentration
1Xist RNA A-repeat AUCG tetraloop hairpinnatural abundance1.0 mM
2sodium phosphatenatural abundance10 mM
3sodium chloridenatural abundance100 mM
4EDTAnatural abundance0.02 mM
5sodium azidenatural abundance0.02 %
6H2Onatural abundance90 %
7D2Onatural abundance10 %
Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0


#NameIsotope labelingTypeConcentration
8Xist RNA A-repeat AUCG tetraloop hairpinnatural abundance1.2 mM
9sodium phosphatenatural abundance10 mM
10sodium chloridenatural abundance100 mM
11EDTAnatural abundance0.02 mM
12sodium azidenatural abundance0.02 %
13D2Onatural abundance100 %
Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0


#NameIsotope labelingTypeConcentration
14Xist RNA A-repeat AUCG tetraloop hairpin[U-98% 13C; U-98% 15N]0.8 ~ 1.2 mM
15sodium phosphatenatural abundance10 mM
16sodium chloridenatural abundance100 mM
17EDTAnatural abundance0.02 mM
18sodium azidenatural abundance0.02 %
19H2Onatural abundance90 %
20D2Onatural abundance10 %
Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0


#NameIsotope labelingTypeConcentration
21Xist RNA A-repeat AUCG tetraloop hairpin[U-98% 13C; U-98% 15N]0.8 ~ 1.2 mM
22sodium phosphatenatural abundance10 mM
23sodium chloridenatural abundance100 mM
24EDTAnatural abundance0.02 mM
25sodium azidenatural abundance0.02 %
26D2Onatural abundance100 %
Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0


#NameIsotope labelingTypeConcentration
27Xist RNA A-repeat AUCG tetraloop hairpinnatural abundance1.2 mM
28sodium phosphatenatural abundance10 mM
29sodium chloridenatural abundance100 mM
30EDTAnatural abundance0.02 mM
31sodium azidenatural abundance0.02 %
32filamentous bacteriophage Pf1natural abundance18 mg/mL
33D2Onatural abundance100 %
Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0, Details sample 50% isotope labeled, 50% unlabeled


#NameIsotope labelingTypeConcentration
34Xist RNA A-repeat AUCG tetraloop hairpin[U-98% 13C; U-98% 15N]0.4 mM
35Xist RNA A-repeat AUCG tetraloop hairpinnatural abundance0.4 mM
36sodium phosphatenatural abundance10 mM
37sodium chloridenatural abundance100 mM
38EDTAnatural abundance0.02 %
39sodium azidenatural abundance0.02 mM
40H2Onatural abundance90 %
41D2Onatural abundance10 %

Coupling constant
42 J values in 1 lists
Field strength (1H) 600 MHz, Pressure 1 atm, Temperature 298 K, pH 6.0 Detail
RDC
29 RDC values in 1 lists
Field strength (1H) 600 MHz, Pressure 1 atm, Temperature 298 K, pH 6.0 Detail
Release date
2011-08-16
Citation 1
¹H, ¹³C, ¹⁵N and ³¹P chemical shift assignments of a human Xist RNA A-repeat tetraloop hairpin essential for X-chromosome inactivation
Duszczyk, M.M., Sattler, M.
Biomol. NMR Assign. (2012), 6, 75-77, PubMed 21779925 , DOI 10.1007/s12104-011-9328-z ,
Citation 2
The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization
Duszczyk, M.M., Wutz, A., Rybin, V., Sattler, M.
PLoS Biol
Related entities 1. AUCG tetraloop hairpin, : 1 entities Detail
Experiments performed 22 experiments Detail
nullKeywords A-repeats, NMR, X-Inactivation, Xist RNA