BMRB Entry 35021

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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/BMR35021
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
Beyond single-state RNA structural biology: MD/NMR description of temperature-sensitive dynamic RNA ensembles - GCAA ARIA 1+3 motif
Deposition date:
2025-10-11
Original release date:
2026-06-30
Authors:
Leopold, D.; Oxenfarth, A.; Thomasen, F.; Kuemmerer, F.; Schnieders, R.; Pinter, G.; Wacker, A.; Jonker, H.; Fuertig, B.; Richter, C.; Lindorff-Larsen, K.; Schwalbe, H.
Citation:

Citation: Leopold, D.; Oxenfarth, A.; Thomasen, F.; Kummerer, F.; Schnieders, R.; Pinter, G.; Wacker, A.; Jonker, H.; Furtig, B.; Richter, C.; Lindorff-Larsen, K.; Schwalbe, H.. "Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of GAAG and GCAA tetraloops. "  RNA ., .-. (2026).
PubMed: 42215280

Assembly members:

Assembly members:
entity_1, polymer, 14 residues, 4500.763 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: GGCACGCAAGUGCC

Data sets:
Data typeCount
13C chemical shifts91
15N chemical shifts23
1H chemical shifts108
31P chemical shifts14

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 - 4500.763 Da.

1   GGCACGCAAG
2   UGCC

Samples:

sample_1: RNA hairpin with GCAA tetraloop 0.6 mM; potassium phosphate 50 mM; DSS 50 uM

sample_2: RNA hairpin with GCAA tetraloop 0.7 mM; potassium phosphate 50 mM; DSS 50 uM

sample_3: RNA hairpin with GCAA tetraloop, [U-13C; U-15N], 0.5 mM; potassium phosphate 50 mM; DSS 50 uM

sample_4: RNA hairpin with GCAA tetraloop, [U-13C; U-15N], 0.7 mM; potassium phosphate 50 mM; DSS 50 uM

sample_5: RNA hairpin with GCAA tetraloop, [U-13C; U-15N], 0.2 mM; potassium phosphate 50 mM; DSS 50 uM

sample_6: RNA hairpin with GCAA tetraloop, [U-13C; U-15N], 0.2 mM; potassium phosphate 50 mM; DSS 50 uM; Pf1 phage 20 mg/mL

sample_conditions_1: ionic strength: 50 mM; pH: 6.4; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_6anisotropicsample_conditions_1
2D 1H-15N HSQCsample_5isotropicsample_conditions_1
2D 1H-15N HSQCsample_6anisotropicsample_conditions_1
3D qHCPsample_3isotropicsample_conditions_1
2D qHCPsample_3isotropicsample_conditions_1
2D P-FIDSsample_3isotropicsample_conditions_1
3D HCC-TOCSY-CCH-E.COSYsample_3isotropicsample_conditions_1
2D HNN-COSYsample_4isotropicsample_conditions_1
2D gamma HCCHsample_3isotropicsample_conditions_1
2D gamma HCNCHsample_3isotropicsample_conditions_1
2D gamma HCPsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_4isotropicsample_conditions_1
2D HCNsample_4isotropicsample_conditions_1
3D forward directed HCCH-TOCSYsample_3isotropicsample_conditions_1
3D HCPsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

TopSpin v4.2.0, Bruker Biospin - collection, processing

NMRFAM-SPARKY v1.470, NMRFAM-SPARKY - chemical shift assignment, peak picking

PALES, Zweckstetter and Bax - data analysis

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

ARIA, Linge, O'Donoghue and Nilges - structure calculation

NMR spectrometers:

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