BMRB Entry 16654

Name: Solution structure of the human mitochondrial tRNAMet ASL containing the 5-formylcytidine modification in position 34
Published: 2011-06-01

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PDB ID: 2kry
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16654
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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 mitochondrial tRNAMet ASL containing the 5-formylcytidine modification in position 34

Deposition date:

2009-12-23

Original release date:

2011-06-01

Authors:

Bilbille, Yann; Agris, Paul

Citation:

Citation: Bilbille, Yann; Gustilo, Estella; Harris, Kimberly; Jones, Christie; Lusic, Hrvoje; Kaiser, Robert; Delaney, Michael; Spremulli, Linda; Deiters, Alexander; Agris, Paul. "The human mitochondrial tRNAMet: structure/function relationship of a unique modification in the decoding of unconventional codons." J. Mol. Biol. 406, 257-274 (2011).
PubMed: 21168417

Assembly members:

Assembly members:
RNA_(5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(N)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3'), polymer, 17 residues, 5268.217 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):
RNA_(5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(N)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3'): XCGGGCCXAUACCCCGA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	130

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R((PSU)PCPGPGPGPCPCP(N)PAPUPAPCPCPCPCPGP*A)-3')	1

Entities:

Entity 1, RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(N)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3') 17 residues - 5268.217 Da.

1

PSU

C

G

C

N

A

U

2

A

C

G

A

Samples:

sample_1: RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(N)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3') 1.0 mM; phosphate buffer 20 mM

sample_2: RNA (5'-R(*(PSU)P*CP*GP*GP*GP*CP*CP*(N)P*AP*UP*AP*CP*CP*CP*CP*GP*A)-3') 1 mM; phosphate buffer 20 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-31P HETCOR	sample_2	isotropic	sample_conditions_1

Software:

xwinnmr, Bruker Biospin - collection

TOPSPIN, Bruker Biospin - collection

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

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

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

CNS v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

Varian INOVA 600 MHz
Bruker Avance 500 MHz