BMRB Entry 34483

Name: Constitutive decay element CDE1 from human 3'UTR
Published: 2020-05-25

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34483

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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: Constitutive decay element CDE1 from human 3'UTR

Deposition date: 2020-01-27 Original release date: 2020-05-25

Authors: Schwalbe, H.; Binas, O.

Citation: Binas, O.; Tants, J.; Peter, S.; Janowski, R.; Davydova, E.; Braun, J.; Niessing, D.; Schwalbe, H.; Weigand, J.; Schlundt, A.. "Structural basis for the recognition of transiently structured AU-rich elements by Roquin" Nucleic Acids Res. ., .-. (2020).

Assembly members:
entity_1, polymer, 19 residues, 6009.584 Da.

Natural source: Common Name: Thermosinus carboxydivorans Nor1 Taxonomy ID: 401526 Superkingdom: Bacteria Kingdom: not available Genus/species: Thermosinus carboxydivorans

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GGAAAUUAUAUUAAUUUCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	112
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	unit_1	1

Entities:

Entity 1, unit_1 19 residues - 6009.584 Da.

1

G

A

U

A

U

A

2

U

A

U

C

Samples:

sample_1: CDE1 350 uM; KCl 50 mM; potassium phosphate buffer 25 mM

sample_2: CDE1, [U-99% 13C; U-99% 15N], 300 uM; KCl 50 mM; potassium phosphate buffer 25 mM

sample_conditions_1: ionic strength: 75 mM; pH: 6.2; pressure: 1 bar; temperature: 298 K

sample_conditions_2: ionic strength: 75 mM; pH: 6.2; pressure: 1 bar; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_2
fwHCC-TOCSY-CCH-E.COSY	sample_2	isotropic	sample_conditions_2
3D HCP	sample_2	isotropic	sample_conditions_2
3D HCN	sample_2	isotropic	sample_conditions_2
2D gamma HCN	sample_2	isotropic	sample_conditions_2
2D PFIDS	sample_2	isotropic	sample_conditions_2

Software:

CNS v1.2, Brunger A. T. et.al. - structure calculation

Sparky v3.2, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 800 MHz
Bruker AVANCE III 600 MHz
Bruker AVANCE III 700 MHz