BMRB Entry 36587

Name: Solution structure of a hairpin RNA with the UUCGA loop
Published: 2025-11-04

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PDB ID: 8k8b
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36587
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of a hairpin RNA with the UUCGA loop

Deposition date:

2023-07-29

Original release date:

2025-11-04

Authors:

Ichijo, R.; Kawai, G.

Citation:

Citation: Ichijo, Rika; Kawai, Gota. "NMR analysis of a loop-bulge structure of UUCGA pentaloop." Biochem. Biophys. Res. Commun. 691, 149327-149327 (2024).
PubMed: 38039839

Assembly members:

Assembly members:
RNA (5'-R(*GP*GP*AP*UP*CP*CP*UP*UP*UP*CP*GP*AP*GP*GP*GP*AP*UP*CP*C)-3'), polymer, 19 residues, 6070.633 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 10090 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA (5'-R(*GP*GP*AP*UP*CP*CP*UP*UP*UP*CP*GP*AP*GP*GP*GP*AP*UP*CP*C)-3'): GGAUCCUUUCGAGGGAUCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	60

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 19 residues - 6070.633 Da.

1

G

A

U

C

U

C

2

G

A

G

A

U

C

Samples:

sample_1: RNA (5'-R(*GP*GP*AP*UP*CP*CP*UP*UP*UP*CP*GP*AP*GP*GP*GP*AP*UP*CP*C)-3') 0.36 mM; NaCl 50 mM; Na2HPO4/NaH2PO4 20 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D HOHAHA	sample_1	isotropic	sample_conditions_1

Software:

Sparky, Goddard - chemical shift assignment

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

Sparky, Goddard - peak picking

NMR spectrometers:

Bruker AVANCE NEO 600 MHz