BMRB Entry 51144

Title:
RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics
Deposition date:
2021-10-16
Original release date:
2022-01-20
Authors:
Biedenbander, Thomas; de Jesus, Vanessa; Schmidt-Dengler, Martina; Helm, Mark; Corzilius, Bjoern; Fuertig, Boris
Citation:

Citation: Biedenbander, Thomas; de Jesus, Vanessa; Schmidt-Dengler, Martina; Helm, Mark; Corzilius, Bjorn; Furtig, Boris. "RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics"  Nucleic Acids Res. 50, 2334-2349 (2022).
PubMed: 35137185

Assembly members:

Assembly members:
entity_1, polymer, 77 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: purified from the natural source

Entity Sequences (FASTA):

Data typeCount
13C chemical shifts4
15N chemical shifts28
1H chemical shifts34
H exchange rates183
T1 relaxation values51
T2 relaxation values49
heteronuclear NOE values52

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1tRNAfMet1

Entities:

Entity 1, tRNAfMet 77 residues - Formula weight is not available

1   CGCGGGG4SUGG
2   AGCAGCCUGG
3   H2UAGCUCGUCG
4   GGOMCUCAUAAC
5   CCGAAGAUCG
6   UCGG5MUPSUCAAA
7   UCCGGCCCCC
8   GCAACCA

Samples:

sample_1: tRNAfMet, [U-100% 13C; U-100% 15N], 530 uM; H2O 93%; D2O, [U-100% 2H], 7%; DSS 250 mM; potassium phosphate 25 mM; potassium chloride 200 mM

sample_conditions_1: ionic strength: 0.2 M; pH: 6.4; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.2 M; pH: 6.4; pressure: 1 atm; temperature: 310 K

sample_conditions_3: ionic strength: 0.2 M; pH: 6.4; pressure: 1 atm; temperature: 290 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D 15N-separated NOESYsample_1isotropicsample_conditions_1
T1/R1 relaxationsample_1isotropicsample_conditions_1
T1/R1 relaxationsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_3
T2/R2 relaxationsample_1isotropicsample_conditions_1
T2/R2 relaxationsample_1isotropicsample_conditions_2
1H-15N heteronoesample_1isotropicsample_conditions_1
1H-15N heteronoesample_1isotropicsample_conditions_2
2D-HNN-COSYsample_1isotropicsample_conditions_1
2D water selective inversion recoverysample_1isotropicsample_conditions_1

Software:

NMRbox v7.0 - data analysis

DynamicsCenter v2.6 - data analysis

SPARKY v3.114 - chemical shift assignment

TOPSPIN v3.2 - processing

ChimeraX v1.2.5 - Structure visualization

Relax v4.1.3 - data analysis

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker AVANCE NEO 600 MHz
  • Bruker AVANCE NEO 900 MHz
  • Bruker AVANCE III 950 MHz
  • Bruker AVANCE III 800 MHz
  • Bruker Avance 800 MHz