BMRB Entry 28090

Name: 1H, 13C, and 15N chemical shifts for T4 Gene 60 mRNA 5&#039; Stem-Loop
Published: 2021-07-16

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR28090

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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:

1H, 13C, and 15N chemical shifts for T4 Gene 60 mRNA 5' Stem-Loop

Deposition date:

2020-02-29

Original release date:

2021-07-16

Authors:

Capece, Mark; Puglisi, Joseph

Citation:

Citation: O'Loughlin, Sinead; Capece, Mark; Klimova, Mariia; Wills, Norma; Coakley, Arthur; Samatova, Ekaterina; O'Connor, Patrick; Loughran, Gary; Weissman, Jonathan; Baranov, Pavel; Rodnina, Marina; Puglisi, Joseph; Atkins, John. "Polysomes bypass a 50 nucleotide coding gap less efficiently than monosomes due to attenuation of an unstable 5' mRNA stem loop stimulator and enhanced drop-off" J. Mol. Biol. 432, 4369-4387 (2020).
PubMed: 32454154

Assembly members:

Assembly members:
5'_stem_loop, polymer, 30 residues, Formula weight is not available

Natural source:

Natural source: Common Name: T4 bacteriophage Taxonomy ID: 38018 Superkingdom: Viruses Kingdom: not available Genus/species: T4 bacteriophage

Experimental source:

Experimental source: Production method: in vitro transcription Host organism: T7 RNA polymerase Vector: N/A

Entity Sequences (FASTA):

Entity Sequences (FASTA):
5'_stem_loop: GUGCGAAUGUCGCUAUUAUG ACAGACGCAC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	73
15N chemical shifts	44
1H chemical shifts	135

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	5' stem loop	1

Entities:

Entity 1, 5' stem loop 30 residues - Formula weight is not available

1	G	U	G	C	G	A	A	U	G	U
2	C	G	C	U	A	U	U	A	U	G
3	A	C	A	G	A	C	G	C	A	C

Samples:

10%_D2O: 5' stem loop, [U-99% 13C; U-99% 15N], 0.3 mM; sodium phosphate 10 mM; sodium chloride 20 mM

99.99%_D2O: 5' stem loop, [U-99% 13C; U-99% 15N], 0.3 mM; sodium phosphate 10 mM; sodium chloride 20 mM

10%_D2O_conditions: pH: 6.5; pressure: 1 atm; temperature: 298 K

99.99%_D2O_conditions: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	10%_D2O	isotropic	10%_D2O_conditions
2D 1H-15N HSQC	10%_D2O	isotropic	10%_D2O_conditions
2D 1H-15N HNNCOSY	10%_D2O	isotropic	10%_D2O_conditions
3D 1H-15N NOESYHSQC	10%_D2O	isotropic	10%_D2O_conditions
3D HNCCCH	10%_D2O	isotropic	10%_D2O_conditions
2D 1H-1H NOESY	99.99%_D2O	isotropic	99.99%_D2O_conditions
2D 1H-13C HSQC	99.99%_D2O	isotropic	99.99%_D2O_conditions
3D 1H-13C NOESYHSQC	99.99%_D2O	isotropic	99.99%_D2O_conditions
3D HCCH-TOCSY	99.99%_D2O	isotropic	99.99%_D2O_conditions
2D DQF-COSY	99.99%_D2O	isotropic	99.99%_D2O_conditions

Software:

VNMRJ v4.2, Varian - collection, processing

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Agilent VNMRS 800 MHz
Agilent INOVA 600 MHz