BMRB Entry 31217

Name: NMR solution structure of tRNA-Arg-UCU-4-1 anticodon stem loop with m3C modification at position 32
Published: 2025-04-15

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PDB ID: 9ecr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31217
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of tRNA-Arg-UCU-4-1 anticodon stem loop with m3C modification at position 32

Deposition date:

2024-11-15

Original release date:

2025-04-15

Authors:

Berger, K.; Puthenpeedikakkal, A.; Matthews, D.; Fu, D.

Citation:

Citation: Berger, K.; Puthenpeedikakkal, A.; Mathews, D.; Fu, D.. "Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA" J. Mol. Biol. ., .-. (2025).
PubMed: 40158946

Assembly members:

Assembly members:
entity_1, polymer, 17 residues, 5378.247 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CUGGAXUUCUAAUCCAG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	116

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 17 residues - 5378.247 Da.

1

C

U

G

A

JMH

U

C

U

2

A

U

C

A

G

Samples:

sample_1: sodium phosphate 10 mM; tRNA-Arg-UCU-4-1 Anticodon stem-loop with m3C at position 32 200 uM; EDTA 50 uM

sample_conditions_1: ionic strength: 10 mM; pH: 6.3; pressure: 1 atm; temperature: 288 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:

NMRFAM-SPARKY, University of Wisconsin-Madison - chemical shift assignment

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

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

NMR spectrometers:

Bruker AVANCE III 800 MHz