BMRB Entry 31176

Name: Major Conformation of the Internal Loop 5&#039;GGAGUC/3&#039;CUGAGG
Published: 2025-03-26

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PDB ID: 9bxe
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31176
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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:

Major Conformation of the Internal Loop 5'GGAGUC/3'CUGAGG

Deposition date:

2024-05-22

Original release date:

2025-03-26

Authors:

Kennedy, S.; Mathews, D.; Akinyemi, O.

Citation:

Citation: Akinyemi, O.; Kennedy, S.; Mathews, D.. "NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent base pairs determine conformational preference" .

Assembly members:

Assembly members:
entity_1, polymer, 11 residues, 3546.178 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GAGGAGUCUCA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	22
1H chemical shifts	96

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1

Entities:

Entity 1, unit_1 11 residues - 3546.178 Da.

1

G

A

G

A

G

U

C

U

C

2

A

Samples:

sample_1: 5'-GAGGAGUCUCA-3' 2.0 ± 0.2 mM; NaCl 70 mM; NaH2PO4/Na2HPO4 30 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.1; pressure: 1 atm; temperature: 274 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

VNMR v6.1C, Varian - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRFAM-SPARKY v1.2, Lee, Tonelli, Markley - chemical shift assignment, peak picking

Amber vv16, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement, structure calculation

NMR spectrometers:

Varian UNITY INOVA 600 MHz