BMRB Entry 30560

Name: Solution structure of a c-JUN 5&#039; UTR stem-loop associated with specialized cap-dependent translation initiation (WT apical loop)
Published: 2020-07-20

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PDB ID: 6noa
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30560
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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:

Solution structure of a c-JUN 5' UTR stem-loop associated with specialized cap-dependent translation initiation (WT apical loop)

Deposition date:

2019-01-16

Original release date:

2020-07-20

Authors:

Walker, M.; Shortridge, M.; Varani, G.

Citation:

Citation: Walker, M.; Shortridge, M.; Albin, D.; Cominsky, L.; Varani, G.. "Structure of the RNA Specialized Translation Initiation Element that Recruits eIF3 to the 5'-UTR of c-Jun" J. Mol. Biol. 432, 1841-1855 (2020).
PubMed: 31953146

Assembly members:

Assembly members:
entity_1, polymer, 56 residues, 17634.342 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGCAGUAUAGUCCGAACUGC AAAUCUUAUUUUCUUUUCAC CUUCUCUCUAACUGCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	291
15N chemical shifts	12
1H chemical shifts	404

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 56 residues - 17634.342 Da.

1

G

C

A

G

U

A

U

A

G

2

U

C

G

A

C

U

G

C

3

A

U

C

U

A

U

4

U

C

U

C

A

C

5

C

U

C

U

C

U

C

U

A

6

A

C

U

G

C

Samples:

sample_1: RNA, [A,G-98% D3', 4', 5', 5"; C,U-98% D3', 4', 5', 5", 5], 1.0 mM; Sodium Phosphate 20 mM

sample_2: RNA 1.0 mM; Sodium Phosphate 20 mM

sample_3: RNA 1.0 mM; Sodium Phosphate 20 mM

sample_4: RNA 1.0 mM; Sodium Phosphate 20 mM

sample_5: RNA 1.0 mM; Sodium Phosphate 20 mM

sample_6: RNA, [A,G-98% D3', 4', 5', 5"; C,U-98% D3', 4', 5', 5", 5], 1.0 mM; Sodium Phosphate 20 mM

sample_7: RNA, [A,C,G,U-98% 13C, A,C,G,U-98% 15N], 1.0 mM; Sodium Phosphate 20 mM

sample_8: RNA, [A,C,G,U-98% 13C, A,C,G,U-98% 15N], 1.0 mM; Sodium Phosphate 20 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.1; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 20 mM; pH: 6.1; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_5	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_6	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_7	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_8	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_7	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

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

SPARKY, Goddard - peak picking

CcpNMR, CCPN - peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Bruker AvanceIII 800 MHz
Bruker AvanceII 600 MHz