BMRB Entry 27452

Name: NMR resonance assignment for the SAM/SAH binding riboswitch RNA bound to S-Adenosylhomocysteine
Published: 2018-08-09

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PDB ID: 6hag
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27452
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR resonance assignment for the SAM/SAH binding riboswitch RNA bound to S-Adenosylhomocysteine

Deposition date:

2018-04-16

Original release date:

2018-08-09

Authors:

Weickhmann, Anna Katharina; Keller, Heiko; Duchardt-Ferner, Elke; Wunderlich, Christoph; Juen, Michael; Kremser, Johannes; Kreutz, Christoph; Woehnert, Jens

Citation:

Citation: Weickhmann, A Katharina; Keller, Heiko; Duchardt-Ferner, Elke; Strebitzer, Elisabeth; Juen, Michael; Kremser, Johannes; Wurm, Jan Philip; Kreutz, Christoph; Wohnert, Jens. "NMR resonance assignments for the SAM/SAH-binding riboswitch RNA bound to S-adenosylhomocysteine" Biomol. NMR Assign. 12, 329-334 (2018).
PubMed: 30051308

Assembly members:

Assembly members:
env9b, polymer, 43 residues, Formula weight is not available
S-ADENOSYL-L-HOMOCYSTEINE, non-polymer, 384.411 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: recombinant technology Host organism: Escherichia coli Vector: pSP64

Entity Sequences (FASTA):

Entity Sequences (FASTA):
env9b: GUCACAACGGCUUCCUGACG UGGCAGAUUGAAUUAUUGGA GCA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	313
15N chemical shifts	126
1H chemical shifts	318

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	env9b	1
2	SAH	2

Entities:

Entity 1, env9b 43 residues - Formula weight is not available

1

G

U

C

A

C

A

C

G

2

C

U

C

U

G

A

C

G

3

U

G

C

A

G

A

U

G

4

A

U

A

U

G

A

5

G

C

A

Entity 2, SAH - C14 H20 N6 O5 S - 384.411 Da.

1

SAH

Samples:

13C15N: env9b, [U-13C; U-15N], 710 uM; S-Adenosylhomocysteine 2 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

15N: env9b, [U-15N], 910 uM; S-Adenosylhomocysteine 2.5 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

13C15N-U: env9b, [U-13C; U-15N]-Ura, 800 uM; S-Adenosylhomocysteine 1.6 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

seldeut: env9b, [U-5-D1/ribose-3 ,4 ,5 ,5 -D4], 750 uM; S-Adenosylhomocysteine 3 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

13C15N-SAH: env9b 700 uM; S-Adenosylhomocysteine, [U-13C; U-15N], 0.5 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

13C15N-AC: env9b, [U-13C; U-15N]-Ade, [U-13C; U-15N]-Ade, 800 uM; S-Adenosylhomocysteine 2 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

13C15N-G: env9b, [U-13C; U-15N]-Gua, 850 uM; S-Adenosylhomocysteine 2 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

unlab: env9b 1.2 uM; S-Adenosylhomocysteine 4 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

13C15N-AC_D2O: env9b, [U-13C; U-15N]-Ade, [U-13C; U-15N]-Ade, 800 uM; S-Adenosylhomocysteine 2 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

13C15N-U_D2O: env9b, [U-13C; U-15N]-Ura, 800 uM; S-Adenosylhomocysteine 1.6 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

13C15N-G_D2O: env9b, [U-13C; U-15N]-Gua, 850 uM; S-Adenosylhomocysteine 2 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

13C15N-U_13C15N-SAH: env9b, [U-13C; U-15N]-Ura, 480 uM; S-Adenosylhomocysteine, [U-13C; U-15N], 750 mM; potassium phosphate 25 mM; potassium chloride 50 mM; magnesium acetate 2 mM

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

283K: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 283 K

271K: ionic strength: 75 mM; pH: 6.2; pressure: 1 atm; temperature: 271 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	13C15N	isotropic	283K
2D 1H-15N HSQC	13C15N-U	isotropic	283K
2D 1H-15N HSQC	13C15N-AC	isotropic	283K
2D 1H-15N HSQC	13C15N-G	isotropic	283K
2D 1H-15N HSQC NH2 only	15N	isotropic	298K
2D 1H-13C HSQC aliphatic	13C15N	isotropic	298K
2D 1H-13C HSQC aliphatic	13C15N-AC	isotropic	298K
2D 1H-13C HSQC aliphatic	13C15N-U	isotropic	298K
2D 1H-13C HSQC aliphatic	13C15N-G	isotropic	298K
2D 1H-13C HSQC aromatic	13C15N	isotropic	298K
2D 1H-13C HSQC aromatic	13C15N-AC	isotropic	298K
2D 1H-13C HSQC aromatic	13C15N-U	isotropic	298K
2D 1H-13C HSQC aromatic	13C15N-G	isotropic	298K
2D 1H-1H NOESY	unlab	isotropic	298K
3D 1H-13C NOESY aromatic	13C15N-AC	isotropic	298K
3D 1H-13C NOESY aromatic	13C15N-U	isotropic	298K
3D 1H-13C NOESY aromatic	13C15N-G	isotropic	298K
3D 1H-13C NOESY aliphatic	13C15N-AC_D2O	isotropic	298K
3D 1H-13C NOESY aliphatic	13C15N-U_D2O	isotropic	298K
3D 1H-13C NOESY aliphatic	13C15N-G_D2O	isotropic	298K
2D 1H-1H NOESY	unlab	isotropic	271K
3D HCCH-TOCSY	13C15N-AC_D2O	isotropic	298K
3D HCCH-COSY	13C15N-AC_D2O	isotropic	298K
3D HCCH-TOCSY	13C15N-U_D2O	isotropic	298K
3D HCCH-COSY	13C15N-U_D2O	isotropic	298K
3D HCCH-TOCSY	13C15N-G_D2O	isotropic	298K
3D HCCH-COSY	13C15N-G_D2O	isotropic	298K
1D 1H-HS11ECHO	unlab	isotropic	283K
2D 1H-15N HNN-COSY	13C15N	isotropic	283K
2D 1H-13C HNCO	13C15N-G	isotropic	298K
2D 1H-13C HNCO	13C15N-U	isotropic	298K
2D 1H-13C H5C5(C4N)H	13C15N-AC	isotropic	298K
2D 1H-15N HCN aromatic	13C15N-U	isotropic	298K
2D 1H-15N HCN aliphatic	13C15N-U_D2O	isotropic	298K
2D 1H-15N 2bond-HSQC	15N	isotropic	298K
TROSY relayed HCCH-COSY	13C15N-AC_D2O	isotropic	298K
2D 1H-13C long-rangeH8(C8)C5(N1)H1	13C15N-G	isotropic	298K
2D 1H-13C H5C5(C4N)H	13C15N-U	isotropic	298K
2D 1H-15N HCN aromatic	13C15N-AC	isotropic	298K
2D 1H-15N HCN aliphatic	13C15N-AC_D2O	isotropic	298K
2D 1H-15N HCN aromatic	13C15N-G	isotropic	298K
2D 1H-15N HCN aliphatic	13C15N-G_D2O	isotropic	298K
2D 1H-15N HNN-COSY	13C15N-U_13C15N-SAH	isotropic	283K
2D 1H-15N HSQC	15N	isotropic	271K
2D lr-1H,15N-HSQC	15N	isotropic	298K
2D 1H-13C HSQC aliphatic	13C15N-SAH	isotropic	298K
2D 1H-13C HSQC aromatic	13C15N-SAH	isotropic	298K
3D HCCH-COSY	13C15N-SAH	isotropic	298K

Software:

TOPSPIN v3.2 or 3.5, Bruker - processing

CARA v1.9.1b9, Keller and Wuthrich - chemical shift assignment

NMR spectrometers:

Bruker Avance 950 MHz
Bruker Avance 900 MHz
Bruker Avance 800 MHz
Bruker Avance 700 MHz
Bruker Avance 600 MHz