BMRBj - BMREntryMaster

Found 1 Document (1.528 seconds)

BMRB: 19534

2MF0

Structural basis of the non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex

Authors

Duss, O., Michel, E., Yulikov, M., Schubert, M., Jeschke, G., Allain, F.H.-T.

Assembly

non-coding RNA RsmZ acting as protein sponge: Conformer L of RsmZ(1-72)/RsmE(dimer) 1to3 complex

Entity

1. RsmE (polymer, Thiol state: not present), 59 monomers, 6398.305 × 6 Da Detail

MLILTRKVGE SINIGDDITI TILGVSGQQV RIGINAPKDV AVHREEIYQR IQAGLTAPD

2. RNA (72-MER) (polymer, Thiol state: not present), 72 monomers, 23435.00 Da Detail

UGUCGACGGA UAGACACAGC CAUCAAGGAC GAUGGUCAGG ACAUCGCAGG AAGCGAUUCA UCAGGACGAU GA

Total weight

61824.832 Da

Max. entity weight

23435.0 Da

Source organism

Pseudomonas fluorescens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 48.1 %, Completeness: 15.5 %, Completeness (bb): 7.4 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	15.5 % (280 of 1803)	14.5 % (140 of 965)	16.2 % (120 of 742)	20.8 % (20 of 96)
Backbone	7.4 % (84 of 1142)	7.6 % (42 of 554)	7.9 % (42 of 531)	0.0 % (0 of 57)
Sidechain	27.5 % (196 of 714)	23.8 % (98 of 411)	29.5 % (78 of 264)	51.3 % (20 of 39)
Aromatic	60.9 % (196 of 322)	60.9 % (98 of 161)	60.9 % (78 of 128)	60.6 % (20 of 33)
Methyl	0.0 % (0 of 92)	0.0 % (0 of 46)	0.0 % (0 of 46)

1. RsmE

MLILTRKVGE SINIGDDITI TILGVSGQQV RIGINAPKDV AVHREEIYQR IQAGLTAPD

2. RNA (72-MER)

UGUCGACGGA UAGACACAGC CAUCAAGGAC GAUGGUCAGG ACAUCGCAGG AAGCGAUUCA UCAGGACGAU GA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 1to16 are labeled

#	Name	Isotope labeling	Concentration
1	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
2	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
3	sodium chloride	natural abundance	0.03 mM
4	potassium phosphate	natural abundance	0.05 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 17to40 are labeled

#	Name	Isotope labeling	Concentration
5	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
6	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
7	sodium chloride	natural abundance	0.03 mM
8	potassium phosphate	natural abundance	0.05 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 41to57 are labeled

#	Name	Isotope labeling	Concentration
9	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
10	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
11	sodium chloride	natural abundance	0.03 mM
12	potassium phosphate	natural abundance	0.05 mM

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 58to72 are labeled

#	Name	Isotope labeling	Concentration
13	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
14	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
15	sodium chloride	natural abundance	0.03 mM
16	potassium phosphate	natural abundance	0.05 mM

Sample #5

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 36-44 are labeled

#	Name	Isotope labeling	Concentration
17	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
18	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
19	sodium chloride	natural abundance	0.03 mM
20	potassium phosphate	natural abundance	0.05 mM

Sample #6

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Concentration
21	RNA (72-MER)	natural abundance	0.2 mM
22	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
23	sodium chloride	natural abundance	0.03 mM
24	potassium phosphate	natural abundance	0.05 mM

Chem. Shift Complete2

Sequence coverage: 4.6 %, Completeness: 8.8 %, Completeness (bb): 4.6 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	8.8 % (317 of 3606)	8.3 % (160 of 1930)	9.1 % (135 of 1484)	11.5 % (22 of 192)
Backbone	4.6 % (104 of 2284)	4.6 % (51 of 1108)	4.9 % (52 of 1062)	0.9 % (1 of 114)
Sidechain	15.2 % (217 of 1428)	13.3 % (109 of 822)	16.5 % (87 of 528)	26.9 % (21 of 78)
Aromatic	31.7 % (204 of 644)	31.7 % (102 of 322)	31.6 % (81 of 256)	31.8 % (21 of 66)
Methyl	3.3 % (6 of 184)	3.3 % (3 of 92)	3.3 % (3 of 92)

1. RsmE

MLILTRKVGE SINIGDDITI TILGVSGQQV RIGINAPKDV AVHREEIYQR IQAGLTAPD

2. RNA (72-MER)

UGUCGACGGA UAGACACAGC CAUCAAGGAC GAUGGUCAGG ACAUCGCAGG AAGCGAUUCA UCAGGACGAU GA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 1to16 are labeled

#	Name	Isotope labeling	Concentration
1	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
2	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
3	sodium chloride	natural abundance	0.03 mM
4	potassium phosphate	natural abundance	0.05 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 17to40 are labeled

#	Name	Isotope labeling	Concentration
5	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
6	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
7	sodium chloride	natural abundance	0.03 mM
8	potassium phosphate	natural abundance	0.05 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 41to57 are labeled

#	Name	Isotope labeling	Concentration
9	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
10	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
11	sodium chloride	natural abundance	0.03 mM
12	potassium phosphate	natural abundance	0.05 mM

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 58to72 are labeled

#	Name	Isotope labeling	Concentration
13	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
14	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
15	sodium chloride	natural abundance	0.03 mM
16	potassium phosphate	natural abundance	0.05 mM

Sample #5

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 36-44 are labeled

#	Name	Isotope labeling	Concentration
17	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
18	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
19	sodium chloride	natural abundance	0.03 mM
20	potassium phosphate	natural abundance	0.05 mM

Sample #6

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Concentration
21	RNA (72-MER)	natural abundance	0.2 mM
22	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
23	sodium chloride	natural abundance	0.03 mM
24	potassium phosphate	natural abundance	0.05 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2MF0, Strand ID: A, B, C, D, E, F Detail

Release date

2014-05-19

Citation

Structural basis of the non-coding RNA RsmZ acting as a protein sponge
Duss, O., Michel, E., Yulikov, M., Schubert, M., Jeschke, G., Allain, F.
Nature (2014), 509, 588-592, PubMed 24828038 , DOI 10.1038/nature13271 , Abstract

Related entities 1. RsmE, : 1 : 7 : 111 entities Detail

Related entities 2. RNA (72-MER), : 1 : 1 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 1to16 are labeled

#	Name	Isotope labeling	Concentration
1	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
2	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
3	sodium chloride	natural abundance	0.03 mM
4	potassium phosphate	natural abundance	0.05 mM

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 17to40 are labeled

#	Name	Isotope labeling	Concentration
5	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
6	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
7	sodium chloride	natural abundance	0.03 mM
8	potassium phosphate	natural abundance	0.05 mM

3 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 41to57 are labeled

#	Name	Isotope labeling	Concentration
9	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
10	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
11	sodium chloride	natural abundance	0.03 mM
12	potassium phosphate	natural abundance	0.05 mM

4 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 58to72 are labeled

#	Name	Isotope labeling	Concentration
13	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
14	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
15	sodium chloride	natural abundance	0.03 mM
16	potassium phosphate	natural abundance	0.05 mM

5 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 36-44 are labeled

#	Name	Isotope labeling	Concentration
17	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
18	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
19	sodium chloride	natural abundance	0.03 mM
20	potassium phosphate	natural abundance	0.05 mM

6 2D 1H-13C TROSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 1to16 are labeled

#	Name	Isotope labeling	Concentration
1	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
2	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
3	sodium chloride	natural abundance	0.03 mM
4	potassium phosphate	natural abundance	0.05 mM

7 2D 1H-13C TROSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 17to40 are labeled

#	Name	Isotope labeling	Concentration
5	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
6	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
7	sodium chloride	natural abundance	0.03 mM
8	potassium phosphate	natural abundance	0.05 mM

8 2D 1H-13C TROSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 41to57 are labeled

#	Name	Isotope labeling	Concentration
9	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
10	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
11	sodium chloride	natural abundance	0.03 mM
12	potassium phosphate	natural abundance	0.05 mM

9 2D 1H-13C TROSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 58to72 are labeled

#	Name	Isotope labeling	Concentration
13	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
14	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
15	sodium chloride	natural abundance	0.03 mM
16	potassium phosphate	natural abundance	0.05 mM

10 2D 1H-13C TROSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2, Details segmentally labeled RNA, in which nucleotides 36-44 are labeled

#	Name	Isotope labeling	Concentration
17	RNA (72-MER)	[U-13C; U-15N], segmentally labeled	0.2 mM
18	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
19	sodium chloride	natural abundance	0.03 mM
20	potassium phosphate	natural abundance	0.05 mM

11 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7.2

#	Name	Isotope labeling	Concentration
21	RNA (72-MER)	natural abundance	0.2 mM
22	RsmE	[U-100% 15N; U-80% 2H]	1.2 mM
23	sodium chloride	natural abundance	0.03 mM
24	potassium phosphate	natural abundance	0.05 mM

nullKeywords cooperativity, electron paramagnetic resonance, homo-dimeric proteins, large solution structure, messenger RNA, multiple protein binding sites, non-coding RNA, Protein/RNA, protein sequestration, protein sponge, Pseudomonas aeruginosa, ribosome binding site, RNAse E cleave sites, RNP assembly, translation activation, translation repressor protein, two conformations

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Found 1 Document (1.528 seconds)

BMRB: 19534

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Related entities 1. RsmE, : 1 : 7 : 111 entities Detail

Related entities 2. RNA (72-MER), : 1 : 1 entities Detail

Experiments performed 11 experiments Detail

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