BMRB Entry 17449

Name: Solution Structure of the human Anti-codon Stem and loop(hASL) of transfer RNA Lysine III (tRNALys3)
Published: 2011-03-08

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PDB ID: 2l9e
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17449
MolProbity Validation Chart

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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 the human Anti-codon Stem and loop(hASL) of transfer RNA Lysine III (tRNALys3)

Deposition date:

2011-02-08

Original release date:

2011-03-08

Authors:

Vendeix, Franck; Murphy, Frank; Leszczynska, Grazyna; Cantara, William; Gustilo, Estella; Sproat, Brian; Malkiewicz, Andrzej; Agris, Paul

Citation:

Citation: Vendeix, Franck; Murphy, Frank; Cantara, William; Leszczyska, Grayna; Gustilo, Estella; Sproat, Brian; Malkiewicz, Andrzej; Agris, Paul. "Human tRNA(Lys3)(UUU) Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism." J. Mol. Biol. 416, 467-485 (2012).
PubMed: 22227389

Assembly members:

Assembly members:
RNA_(5'-R(*GP*CP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*UP*CP*UP*GP*C)-3')_, polymer, 17 residues, 5644.569 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA_(5'-R(*GP*CP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*UP*CP*UP*GP*C)-3')_: GCAGACUXUUXAUCUGC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	131

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	tRNALys3UUU	1

Entities:

Entity 1, tRNALys3UUU 17 residues - 5644.569 Da.

1

G

C

A

G

A

C

U

70U

U

2

12A

A

U

C

U

G

C

Samples:

sample_1: tRNALys3UUU 1.50 mM; H2O 90%; D2O 10%

Sample_2: tRNALys3UUU 1.50 mM; D2O 100%

sample_conditions_1: ionic strength: . M; pH: 6.2; pressure: 1 atm; temperature: 275 K

sample_conditions_2: ionic strength: . M; pD: 6.2 pD; pressure: 1 atm; temperature: 295 K

sample_conditions_3: ionic strength: . M; pH: 6.2; pressure: 1 atm; temperature: 295 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_3
2D 1H-1H COSY	Sample_2	isotropic	sample_conditions_2
2D DQF-COSY	Sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	Sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	Sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	Sample_2	isotropic	sample_conditions_2
2D 1H-31P HETCOR	Sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_3

Software:

xwinnmr, Bruker Biospin - collection, processing

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

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - geometry optimization, refinement, structure solution

NMR spectrometers:

Bruker DRX 500 MHz
Varian Unity 600 MHz