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:

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):

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"; 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:

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