BMRB Entry 34038

Name: SINEB2 element of the long non-coding RNA activator of translation AS Uchl1
Published: 2017-09-15

Click here to enlarge.

PDB ID: 5lsn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34038
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

SINEB2 element of the long non-coding RNA activator of translation AS Uchl1

Deposition date:

2016-09-05

Original release date:

2017-09-15

Authors:

Podbevsek, P.; Plavec, J.

Citation:

Citation: Podbevsek, P.; Fasolo, F.; Bon, C.; Cimatti, L.; Reisser, S.; Carninci, P.; Bussi, G.; Zucchelli, S.; Plavec, J.; Gustincich, S.. "Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1" Sci. Rep. 8, 3189-3189 (2018).
PubMed: 29453387

Assembly members:

Assembly members:
entity_1, polymer, 29 residues, 9309.521 Da.

Natural source:

Natural source: Common Name: House Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CCUCGUGGUGGUUGUGAACC ACCAUGUGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	63
15N chemical shifts	18
1H chemical shifts	93

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 29 residues - 9309.521 Da.

1

C

U

C

G

U

G

U

G

2

G

U

G

U

G

A

C

3

A

C

A

U

G

U

G

Samples:

sample_1: RNA (29-MER) 0.5 mM

sample_2: RNA (29-MER) 0.5 mM

sample_3: RNA (29-MER), [U-99% 13C; U-99% 15N], 0.5 mM

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 298 K

sample_conditions_2: pH: 7; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D HCN	sample_3	isotropic	sample_conditions_1

Software:

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure calculation

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

SPARKY, Goddard - chemical shift assignment

VNMR, Varian - collection

NMR spectrometers:

Agilent VNMRS 600 MHz