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: 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:
entity_1, polymer, 14 residues, 4454.683 Da.
Natural source: Common Name: not available Taxonomy ID: 2086595 Superkingdom: not available Kingdom: not available Genus/species: synthetic RNA
Experimental source: Production method: chemical synthesis
Entity Sequences (FASTA):
entity_1: GGCAGCUUGCUGCC
- assigned_chemical_shifts
Data type | Count |
13C chemical shifts | 93 |
15N chemical shifts | 10 |
1H chemical shifts | 122 |
31P chemical shifts | 13 |
Additional metadata:
Assembly:
Entity Assembly ID | Entity Name | Entity ID |
---|---|---|
1 | unit_1 | 1 |
Entities:
Entity 1, unit_1 14 residues - 4454.683 Da.
1 | G | G | C | A | G | C | U | U | G | C | ||||
2 | U | G | C | C |
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:
Name | Sample | Sample state | Sample conditions |
---|---|---|---|
2D 1H-1H NOESY | sample_3 | isotropic | sample_conditions_1 |
2D 1H-13C HSQC | sample_6 | anisotropic | sample_conditions_1 |
2D 1H-13C HSQC | sample_7 | isotropic | sample_conditions_1 |
2D 1H-15N HSQC | sample_7 | isotropic | sample_conditions_1 |
2D 1H-15N HSQC | sample_6 | anisotropic | sample_conditions_1 |
3D qHCP | sample_2 | isotropic | sample_conditions_1 |
2D qHCP | sample_2 | isotropic | sample_conditions_1 |
2D P-FIDS | sample_2 | isotropic | sample_conditions_1 |
3D HCC-TOCSY-CCH-E.COSY | sample_2 | isotropic | sample_conditions_1 |
2D HNN-COSY | sample_1 | isotropic | sample_conditions_1 |
2D gamma HCCH | sample_2 | isotropic | sample_conditions_1 |
2D gamma HCNCH | sample_2 | isotropic | sample_conditions_1 |
2D gamma HCP | sample_2 | isotropic | sample_conditions_1 |
2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
2D HCN | sample_1 | isotropic | sample_conditions_1 |
3D forward directed HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
3D HCP | sample_2 | isotropic | sample_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