BMRB Entry 51079

Name: Structural effects of m6A modification of the Xist A repeat AUCG tetraloop and its recognition by YTHDC1
Published: 2022-02-18

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PDB ID: 7pof
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51079
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Structural effects of m6A modification of the Xist A repeat AUCG tetraloop and its recognition by YTHDC1 PubMed: 35166835

Deposition date: 2021-09-07 Original release date: 2022-02-18

Authors: Jones, Alisha

Citation: Jones, Alisha; Tikhaia, Ekaterina; Mourao, Andre; Sattler, Michael. "Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1" Nucleic Acids Res. 50, 2350-2362 (2022).

Assembly members:
entity_1, 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):
entity_1: GGCGCXUCGGCGCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	50
15N chemical shifts	8
1H chemical shifts	86

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	(m6A)UCG tetraloop hairpin	1

Entities:

Entity 1, (m6A)UCG tetraloop hairpin 14 residues - Formula weight is not available

1

G

C

G

C

6MZ

U

C

G

2

C

G

C

Samples:

sample_1: Xist (m6A)UCG tetraloop hairpin 1 mM; sodium chloride 25 mM; sodium phosphate 25 mM

sample_2: Xist (m6A)UCG tetraloop hairpin 1 mM; sodium chloride 25 mM; sodium phosphate 25 mM

sample_3: Xist (m6A)UCG tetraloop hairpin, [U-100% 13C; U-100% 15N], 1 mM; sodium chloride 25 mM; sodium phosphate 25 mM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: pH: 6.5; pressure: 1 atm; temperature: 280 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY-HMQC	sample_3	isotropic	sample_conditions_1
HNN-COSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2

Software:

CcpNMR v2.4 - chemical shift assignment

TOPSPIN v3.5 pl6 - collection, processing

X-PLOR NIH v3.1 - refinement, structure solution

NMR spectrometers:

Bruker AVANCE III 950 MHz
Bruker AVANCE III 900 MHz