BMRB Entry 51127

Name: A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript
Published: 2022-10-05

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PDB ID: 7shx
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51127
MolProbity Validation Chart

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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:

A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript

Deposition date:

2021-10-05

Original release date:

2022-10-05

Authors:

Sharma, Shrikant; Varani, Gabriele

Citation:

Citation: Sharma, Shrikant; Pisignano, Giuseppina; Merulla, Jessica; Catapano, Carlo; Varani, Gabriele. "A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript" Nucleic Acids Res. 50, 11331-11343 (2022).
PubMed: 36243981

Assembly members:

Assembly members:
entity_1, polymer, 94 residues, Formula weight is not available

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: enzymatic synthesis by invitro transcription Host organism: T7 RNA polymerase

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGACCCAUAACCCACCUAGA CCCUAGCUUCGGCUAGAGGG UCAACGCGAAAGCGAGGCCG GGUGGGCGGGUACGUCCGCC CUGGGGAGGGGUCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	530
15N chemical shifts	29
1H chemical shifts	654

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	paRNA	1

Entities:

Entity 1, paRNA 94 residues - Formula weight is not available

1

G

A

C

A

U

A

2

C

A

C

U

A

G

A

3

C

U

A

G

C

U

C

4

G

C

U

A

G

A

G

5

U

C

A

C

G

C

G

A

6

A

G

C

G

A

G

C

G

7

G

U

G

C

G

8

U

A

C

G

U

C

G

C

9

C

U

G

A

G

10

G

U

C

Samples:

sample_1: paRNA, [U-99% 13C; U-99% 15N], 0.75 mM; paRNA, [U-99% 13C; U-99% 15N], 0.75 mM; Sodium phosphate 20 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D 1H	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

NMRFAM-SPARKY - chemical shift assignment

NMR spectrometers:

Bruker Avance 600 and 800 MHz MHz