BMRB Entry 34796

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34796
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Title:
Integrated NMR/MD structure determination of a dynamic and thermodynamically stable CUUG RNA tetraloop
Deposition date:
2023-02-17
Original release date:
2023-07-13
Authors:
Oxenfarth, A.; Kuemmerer, F.; Bottaro, S.; Schnieders, R.; Pinter, G.; Jonker, H.; Fuertig, B.; Richter, C.; Blackledge, M.; Lindorff-Larsen, K.; Schwalbe, H.
Citation:

Citation: Oxenfarth, A.; Kuemmerer, F.; Bottaro, S.; Schnieders, R.; Pinter, G.; Jonker, H.; Fuertig, B.; Richter, C.; Blackledge, M.; Lindorff-Larsen, K.; Schwalbe, H.. "Integrated NMR/MD structure determination of a dynamic and thermodynamically stable CUUG RNA tetraloop"  .

Assembly members:

Assembly members:
entity_1, polymer, 14 residues, 4454.683 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 2086595   Superkingdom: not available   Kingdom: not available   Genus/species: synthetic RNA

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGCAGCUUGCUGCC

Data sets:
Data typeCount
13C chemical shifts93
15N chemical shifts10
1H chemical shifts122
31P chemical shifts13

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 14 residues - 4454.683 Da.

1   GGCAGCUUGC
2   UGCC

Samples:

sample_1: RNA hairpin with CUUG tetraloop, [U-13C; U-15N]-Ade,-Cyt,-Gua,-Ura, 0.64 mM; potassium phosphate 10 mM; EDTA 1 mM; DSS 50 uM

sample_2: RNA hairpin with CUUG tetraloop, [U-13C; U-15N]-Ade,-Cyt,-Gua,-Ura, 1.26 mM; potassium phosphate 10 mM; EDTA 1 mM; DSS 50 uM

sample_3: RNA hairpin with CUUG tetraloop 0.98 mM; potassium phosphate 10 mM; EDTA 1 mM; DSS 50 uM

sample_4: RNA hairpin with CUUG tetraloop 0.86 mM; potassium phosphate 10 mM; EDTA 1 mM; DSS 50 uM

sample_6: RNA hairpin with CUUG tetraloop, [U-13C; U-15N]-Ade,-Cyt,-Gua,-Ura, 0.2 mM; potassium phosphate 10 mM; EDTA 1 mM; DSS 50 uM; Pf1 phage 20 mg/mL

sample_7: RNA hairpin with CUUG tetraloop, [U-13C; U-15N]-Ade,-Cyt,-Gua,-Ura, 0.2 mM; potassium phosphate 10 mM; EDTA 1 mM; DSS 50 uM

sample_conditions_1: ionic strength: 13 mM; pH: 6.4; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_6anisotropicsample_conditions_1
2D 1H-13C HSQCsample_7isotropicsample_conditions_1
2D 1H-15N HSQCsample_7isotropicsample_conditions_1
2D 1H-15N HSQCsample_6anisotropicsample_conditions_1
3D qHCPsample_2isotropicsample_conditions_1
2D qHCPsample_2isotropicsample_conditions_1
2D P-FIDSsample_2isotropicsample_conditions_1
3D HCC-TOCSY-CCH-E.COSYsample_2isotropicsample_conditions_1
2D HNN-COSYsample_1isotropicsample_conditions_1
2D gamma HCCHsample_2isotropicsample_conditions_1
2D gamma HCNCHsample_2isotropicsample_conditions_1
2D gamma HCPsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D HCNsample_1isotropicsample_conditions_1
3D forward directed HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCPsample_2isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection, processing

Sparky vNMRFAM, Sparky - chemical shift assignment, peak picking

GROMACS, https://www.gromacs.org/ - structure calculation

PALES, Zweckstetter and Bax - data analysis

NMR spectrometers:

  • Bruker AVANCE 600 MHz
  • Bruker AVANCE III HD 700 MHz
  • Bruker AVANCE 800 MHz
  • Bruker AVANCE 900 MHz
  • Bruker AVANCE II 600 MHz