BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 30560

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: Walker, M.; Shortridge, M.; Albin, D.; Cominsky, L.; Varani, G.. "Solution structure of a c-JUN 5' UTR stem-loop associated with specialized cap-dependent translation initiation"  . ., .-..

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

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

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GGCAGUAUAGUCCGAACUGC AAAUCUUAUUUUCUUUUCAC CUUCUCUCUAACUGCC

Data sets:
Data typeCount
13C chemical shifts291
15N chemical shifts12
1H chemical shifts404

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 56 residues - 17634.342 Da.

1   GGCAGUAUAG
2   UCCGAACUGC
3   AAAUCUUAUU
4   UUCUUUUCAC
5   CUUCUCUCUA
6   ACUGCC

Samples:

sample_1: RNA, [A,G-98% D3', 4', 5', 5, 5]" ± $entity_1 1; . natural abundance; .

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, 5]" ± $entity_1 1; . natural abundance; .

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_2
2D 1H-1H NOESYsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_5isotropicsample_conditions_2
2D 1H-1H NOESYsample_6isotropicsample_conditions_1
2D 1H-1H TOCSYsample_4isotropicsample_conditions_1
2D 1H-13C HSQCsample_7isotropicsample_conditions_1
2D 1H-15N HSQCsample_8isotropicsample_conditions_2
3D 1H-13C NOESYsample_7isotropicsample_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